indicated in shaded lowercase letters (hg19, Chr2: 217,955, ,957,266).

Transcription

1 Legend for Supplementary Figures Figure S1: Sequence of 2q35 encnv. The DNA sequence of the 1,375bp 2q35 encnv is indicated in shaded lowercase letters (hg19, Chr2: 217,955, ,957,266). Figure S2: Determining allelic linkage in MCF7 cells using a transactivator-fused CRISPR system. To evaluate the allelic linkage of the 2q35 encnv relative to the IGFBP5 intronic marker SNP (rs ), we utilized a transactivator-fused nuclease defective CRISPR system (CRISPR-TA) {Perez-Pinera et al, Nature Methods 2013} to activate relevant genomic sites in 2q35 using site-specific targeting guide RNAs. Targeting the CRISPR-TA to two equivalent promoter sites (i.e. each can bind both IGFBP5 alleles at the promoter) we observe no significant change in allelic balance (Purple; P=0.52 and 0.91). When targeting to the ERE at the 2q35 encnv (i.e. bind both alleles of this ERE) we observe a significant increase in relative IGFBP5-A expression (Orange; P=0.004). When targeting the CRISPR-TA to the wildtype sequence of the remaining encnv allele (i.e. TA binds within the wildtype allele at the distal encnv on only one allele) we observe no significant shift in the allelic balance (Blue; P=0.489 and 0.101). Due to the nature of the targeting guide RNA and lack of sequence specificity within a 20bp region overlapping the deletion junction, we are unable to target the variant allele directly. Guide RNA sequences are: encnv site 1: TAGATGGATCCCTCAGAAAT; encnv site 2: CCATAGACAGGTCTTTTTTG; ERE: CTGAACTGTCCTCAAGTTCT; IGFBP5 Promoter site 1: CTACAAACTGGCTGGCAGCC; IGFBP5 Promoter site 2: GTTTGTACTGCAAAGCTCCT. Black bars represent the mean; P-values are a two-tailed T-test, as marked.

2 Supplementary Figure 3a: Forest plot for 2q35 encnv. Meta-analysis of the imputed 2q35 encnv in BCAC datasets (GWAS alone, top; icogs alone, bottom; and all datasets, combined ). Heterogeneity (i 2 and P-het) are indicated in the inset box. Supplementary Figure 3b: Forest plot for 2q35 encnv linked SNP, rs Metaanalysis of genotyped SNP rs in BCAC datasets (GWAS alone, top; icogs alone, bottom; and all datasets, combined ). Heterogeneity (i 2 and P-het) are indicated in the inset box. Legend for Supplementary Tables Supplementary Table 1: Characteristics of 2,544 WCHS participants with 2q35 encnv genotype. Population characteristics for the WCHS samples with 2q35 encnv genotype are indicated for European American and African American individuals. Supplementary Table 2: Association of 2q35 encnv genotype with overall breast cancer risk by menopausal status in WCHS. Associations of 2q35 encnv genotype with breast cancer in the WCHS samples are indicated for European American and African American individuals, and stratified by menopausal status. Supplementary Table 3: Association of 2q35 encnv genotype with overall breast cancer risk by estrogen receptor status in WCHS. Associations of 2q35 encnv genotype

3 with breast cancer in the WCHS samples are indicated for European American and African American individuals, and stratified by estrogen receptor status. Supplementary Table 4: Association of imputed 2q35 encnv genotype and linked variants with breast cancer risk overall and by estrogen receptor status in BCAC datasets. Associations of variants in the 2q35 encnv LD block with breast cancer in the icogs dataset overall and stratified by estrogen receptor status. Supplementary Table 5: Conditional analysis of 2q35 encnv with previously reported loci. Results of conditional analyses for imputed 2q35 encnv genotype with previously identified 2q35 breast cancer risk loci, rs and rs Supplementary Table 6: Primer sequences used in experiments. Indicated are primer sequences grouped by experiment.

4 Figure S1: Sequence of 2q35 encnv. The DNA sequence of the 1,375bp 2q35 encnv is indicated in shaded lowercase letters (hg19, Chr2: 217,955, ,957,266). AATTCTCGAGGACGGAAGTGGCAGAAAACTGTATGAGTAAGGAGTGAAAGAGGAAGCCTTTTATTTTCTCCCTGGAGATC AGAACCAGAGCAGCTACGATAAGAAAGTAGGTTGGAGACGCAAGAGAATTTGCATAAGTGTTTCTGAGAACCATATATTT TCATCCCCTTTAGTGTCTTCAGAGCGGCATGAATAATAAATAGAATTCCATCTTTGTTACTTTCAGTTTGGGGACATTGC TGCTTAAATCTGAAACTGCTCTGAGACTGAAGCACATGGGTCTCTGAGTTTATTAGGGTTACACATAGACAATGAAACAC ATGGTCAGAGAGGTTAAGAGAATGATCTATTAATAGTAGAACCTAACTACTGCTTAAAGCCCTATGCCATGCCTTATCCT TCCACTTCACCCTACAAAACTAAAGTGTATACATTTGTTTCAGTTGTTGCTGCTTGCTTGTTTGCTTTTCTGTTTTGAGC TTTTCTTTTCTTTTGTGGAGGGTAAGAAAGGTAAGCTTGTGTGCTCTTCCCAGTTCATGGAAGCTCGTCAAGTTTTCAGT TTGCATTATCAAGCAAATGCTTTGCAGGATCAGGAGTTTTTAAATTTCTTTATATTTTTTATTTTCCTTATTTTTGGCAC CTTATCCAAGACCTGTGAGTCCCTCTGGGCTGTGTGTCTGAGAAGTGATAATTGAATTTCTCAGGGTGCAAGTCACTGGG AAGCTGAGTTTGCGGCATGTTAGCTTGGTATCTCTCTTTATTTCTGAGCACCCCCACCCTCTCTCAGGCCAAGTCACAGC TGAATGCTTCACATTAAAACGCACAAAAACATGAATCCGTAGGGCAATACACCAATGGAATCTTTAGGATTCAGACTCAT AATAGTTCATCTCTTGCTTGGTCTGCCCTGAGGTTCTGAGTGAGATTATCCTGCTTGCTCACACCTTATTAATTTTGATT TATCTAAGGGAGAGATGTAGAAATGTCCTCACCTATGTTTGTGCTTCAGGTAAGTCAAAGATGTTTGTTTCTATCTACTT AAGAGAGTAAACAACTGAGTCTTGGTATAGTCAGGCATAGGCTTTggtggagagatttggatgcttaggctcctatttga cagaaagcaaggcctggagctgagaaccccaaacaggtaatccttgggaaggtatgtctgggtgtcacggtagtcagctg agaatgtaaagtgctgcctatggctaagggtatgggatagactgttgcctacttgaccctctctgcagtgtctacagtga gttttgtttgtttgttttttaatgtaagtggttgggaagaggagatcgatgggaaagttacaaaagaaacaggaatttcc aaagaatctgagaacttagagaggtgagagaagagagaaaggaaaagcactgcccagagaggagaggccaagttggagca tccagaaaggcctgccacgttcccctgtgacagccctgctctgacagggtgagggcctgggacaggaggagatagaagga agggagaatggaagggaggaaatgcaaggattcgagcctcctccacagataggaaaaatttagaccagggatgctgatgt cgcttactatgatttattgtcattgtgtgggtgttcacacagggtgtacacactttccattctcccaggtccatgtgatc tggactctaatctgagggatgatctgacaacaacaacaacagctgcaaaaatgtagaaggaaccccagaagctgatggag ttgaacacctgctctaatggaggcagaacatgggaaagtggattgaaaatgaccaaaaagaaaaaatttacctttagttt cacaaatcccctgggctgcatggggccatgatccgcatctgggggtaaaatatcagacatgattatgttttgttttcctt ctaattgaaagactagaatataaaacggaaatgaatggtgagaggctggcatatccagaaaacagagaatagatcttcac agatatactgaaaatccatggggagagatgtggcttgatggtggagacaggcgaagccatgaagggctgacaagtcatga caagagtggtgtgttttaccctgtaagtcatagggactcactgatgacttttgagcaggggagaaacatgatcaggtttg ggtttgagaacaatcattctggtttcagggtggcaagtgcagcagaggatggcaggagggcatggaaaaagggatacatc tccattccatagcattgaacactgaactgtcctcaagttctaggactgcagtgcctctggtccttccccagtggccagac ttcctaaatggtcagaactgagctccatagacaggtcttttttgcggctaacgtccaaccactttctgacttagatggat ccctcagaaatgggagcaaaagctcttctaagttccttgtacatacatatcaggcatgaaggtgggatattctcagaatc CCAGGAGGGAACAGTGATTGAGGAAACAAGGGCTCCAGGAAAAACATGCTTGGGATTTTATGGAAGAGTTCTGGATTCTG GAAGAAACTGGAAAAGAAGGAAGTGATCTGTCACTGGGGAAAAAAAATCAACATTTCTGGTTCTACCTTCTTAAATATAA GATTTTATCTCATCATAAAGGTCACAGTGACCTGGAAAATGAGGACTTCCATCACATTTGTACAGCTTCCCAGGTTTTAC AGCTTATTTTCACAAGTGTACTTTATTCCATCCTCATAACTTCCTTGTGTGTTTGGTCAGCTAGATAAACTCTCAAAAGC CTCAGTGTCCTTGTTTGTTCAGAAATGGGATTAGTATGTGGCCTGCTCACAGTCAGATGGCTAATCAGCCCAGAGCCAGA AGCTGCTTGCAGGCTAATGGCCAAGCCTATCTCTCAGCACTGCCTCTGCAGCAGGCAAGGCTTGGCCATGTGTGGCTGTG TGGCTGTGTGGCTGTGTGGCTGTGTGGCCGTGTGGCCGTGTGGCCGTGCCGCTGTGCGACTGTGTGGCCGTGCGGCCGTG CGGCTGTGCGGCTGTGCGGCTGTGCGGCTGTGCGGCCGTGTGGCCGTGTGGTTGTGTGGCTGTGTGGTTGTGTGGCTGTG TGGTTGTGTGGCTGTGTGGCTGTGTGGCTGTGTGCTTGCTTGCATGTGAGTTTGCAAGTGATGAAGGGGAAGCGGGTAGC TGTTAGGG

5 100% A Allelic IGFBP5 expression by CRISPR-TA targeting site Allele balance rs A/C 50% A 50% C p=0.003 p=0.015 p=0.52 p=0.91 p=0.004 p=0.489 p= % C encnv site1 encnv site 2 ERE Promoter site 1 Promoter site 2 noguide IGFBP5-A wildtype IGFBP5-C variant ~400 Kb Lower panel scale approximate Figure S2: Determining allelic linkage in MCF7 cells using a transactivator-fused CRISPR system. To evaluate the allelic linkage of the 2q35 encnv relative to the IGFBP5 intronic marker SNP (rs ), we utilized a transactivator-fused nuclease defective CRISPR system (CRISPR-TA) {Perez-Pinera et al, Nature Methods 2013} to activate relevant genomic sites in 2q35 using site-specific targeting guide RNAs. Targeting the CRISPR-TA to two equivalent promoter sites (i.e. each can bind both IGFBP5 alleles at the promoter) we observe no significant change in allelic balance (Purple; P=0.52 and 0.91). When targeting to the ERE at the 2q35 encnv (i.e. bind both alleles of this ERE) we observe a significant increase in relative IGFBP5-A expression (Orange; P=0.004). When targeting the CRISPR-TA to the wildtype sequence of the remaining encnv allele (i.e. TA binds within the wildtype allele at the distal encnv on only one allele) we observe no significant shift in the allelic balance (Blue; P=0.489 and 0.101). Due to the nature of the targeting guide RNA and lack of sequence specificity within a 20bp region overlapping the deletion junction, we are unable to target the variant allele directly. Guide RNA sequences are: encnv site 1: TAGATG- GATCCCTCAGAAAT; encnv site 2: CCATAGACAGGTCTTTTTTG; ERE: CTGAACTGTCCTCAAGTTCT; IGFBP5 Promoter site 1: CTA- CAAACTGGCTGGCAGCC; IGFBP5 Promoter site 2: GTTTGTACTGCAAAGCTCCT. Black bars represent the mean; P-values are a two-tailed T-test, as marked.

6 Figure S3: Forest plot for 2q35 encnv. Meta-analysis of the imputed 2q35 encnv in BCAC datasets (GWAS alone, top; icogs alone, bottom; and all datasets, combined ). Heterogeneity (i^2 and p-het) are indicated in the inset box. GWAS ABCFS_GWAS BBCS_GWAS DFBBCS_GWAS GCHBOC_GWAS HEBCS_GWAS MARIE_GWAS SASBAC_GWAS UK2_GWAS Combined_GWAS icogs ABCFS ABCS BBCC BBCS BIGGS BSUCH CECILE CGPS CNIO BCS CTS DEMOKRITOS ESTHER GENICA HEBCS HMBCS KARBAC KBCP kconfab/aocs LMBC MARIE MBCSG MCBCS MCCS MEC MTLGEBCS NBCS NBHS_TN OBCS OFBCR ORIGO OSU PBCS pkarma RBCS RPCI SASBAC SBCS SEARCH SKK SZBCS UKBGS icogs_all Combined p het icogs=0.04 I^2 icogs= Odds Ratio

7 Figure S4: Forest plot for 2q35 encnv linked SNP, rs Meta-analysis of genotyped SNP rs in BCAC datasets (GWAS alone, top; icogs alone, bottom; and all datasets, combined ). Heterogeneity (i^2 and p-het) are indicated in the inset box. GWAS ABCFS_GWAS BBCS_GWAS DFBBCS_GWAS GCHBOC_GWAS HEBCS_GWAS MARIE_GWAS SASBAC_GWAS UK2_GWAS BPC3_GWAS BCFR_GWAS Combined_GWAS icogs ABCFS ABCS BBCC BBCS BIGGS BSUCH CECILE CGPS CNIO BCS CTS DEMOKRITOS ESTHER GENICA HEBCS HMBCS KARBAC KBCP kconfab/aocs LMBC MARIE MBCSG MCBCS MCCS MEC MTLGEBCS NBCS NBHS_TN OBCS OFBCR ORIGO OSU PBCS pkarma RBCS RPCI SASBAC SBCS SEARCH SKK SZBCS UKBGS icogs_all Combined p het icogs=0.08 I^2 icogs= Odds Ratio

8 Table S1: Characteristics of 2,544 WCHS participants with 2q35 encnv genotyped European American African American Cases Controls Cases Controls N (%) N (%) P a N (%) N (%) Total 613 (100%) 630 (100%) 569 (100%) 732 (100%) P a Proportion of EA Ancestry, mean (std) 96.8% (7.7%) 98.4% (3.7%) < % (16.4%) 14.5% (14.8%) 0.88 Age at interview <30 3 (0.5) 3 (0.5) < (1.6) 15 (2.1) < (10) 92 (14.6) 62 (10.9) 123 (16.8) (31.2) 188 (29.8) 159 (27.9) 242 (33.1) (33.9) 262 (41.6) 208 (36.6) 259 (35.4) (24.5) 85 (13.5) 131 (23) 93 (12.7) Menopausal Status Premenopausal 316 (51.55) 347 (55.08) (47.6) 413 (56.4) Postmenopausal 297 (48.45) 283 (44.92) 298 (52.4) 319 (43.6) Education 12 th grade 18 (2.9) 6 (1) < (14.2) 104 (14.2) 0.30 High school 113 (18.4) 67 (10.6) 173 (30.4) 188 (25.7) Some college 132 (21.5) 117 (18.6) 153 (26.9) 200 (27.3) College graduate 178 (29) 204 (32.4) 101 (17.8) 142 (19.4) Post- graduate degree 172 (28.1) 236 (37.5) 61 (10.7) 98 (13.4) Family history of BrCa No 357 (58.2) 426 (67.6) (68.9) 577 (78.8) < Yes 256 (41.8) 204 (32.4) 177 (31.2) 155 (21.2) Body Mass Index (Kg/m2) < (3.6) 29 (4.6) (1.6) 8 (1.1) < (42.6) 253 (40.2) 99 (17.4) 122 (16.7) 25 - < (25.3) 179 (28.5) 156 (27.5) 209 (28.6) (28.6) 168 (26.7) 304 (53.5) 393 (53.7) Age at menarche <11 59 (9.7) 54 (8.6) (13.5) 83 (11.4) (14.1) 87 (13.9) 93 (16.3) 129 (17.7) (28.5) 167 (26.7) 123 (21.6) 169 (23.2) (47.7) 317 (50.7) 276 (48.5) 349 (47.8) Smoking Satus Current 72 (11.8) 76 (12.1) (13.9) 170 (23.2) Former 222 (36.3) 198 (31.4) 137 (24.1) 149 (20.4) Never 319 (52) 356 (56.5) 353 (62) 413 (56.4) Parity Nulliparous 189 (30.8) 173 (27.5) (15.8) 112 (15.3) (15.3) 117 (18.6) 126 (22.1) 172 (23.5) (31.5) 213 (33.8) 155 (27.2) 196 (26.8) 3 94 (15.3) 94 (14.9) 101 (17.8) 129 (17.6) 4 26 (4.2) 16 (2.5) 49 (8.6) 66 (9) 5 17 (2.8) 17 (2.7) 48 (8.4) 57 (7.8) Age at first pregnancy b (7.8) 26 (5.7) (37.8) 250 (40.4) (26.4) 99 (21.7) 142 (29.7) 174 (28.1) (29) 127 (27.8) 85 (17.8) 92 (14.9) (36.8) 205 (44.9) 71 (14.8) 103 (16.6) AJCC Stage (18.3) 93 (16.3) < I 173 (28.2) 109 (19.2) II 99 (16.2) 122 (21.4) III+ 29 (4.7) 54 (9.5) Missing 200 (32.6) 191 (33.6) Grade 1 98 (16) 29 (5.1) < (25.8) 139 (24.4) (18.6) 185 (32.5) Missing 243 (39.6) 216 (37.9) Estrogen Receptor ER+ 374 (61) 293 (51.5) < ER- 77 (12.6) 140 (24.6) Missing 162 (26.0) 136 (23.9) 2q35 encnv genotype (number of deleted alleles) (94.6) 574 (91.1) (78.6) 533 (72.8) (5.2) 49 (7.8) 117 (20.6) 170 (23.2) 2 1 (0.2) 7 (1.1) 5 (0.9) 29 (3.9) a x 2 test of proportions b among parous women only

9 Table S2: Association of 2q35 encnv genotype with overall breast cancer risk by menopausal status in WCHS c Genotype All Premenopausal Postmenopausal All Women Ca vs Co a OR (95% CI) b P Ca vs Co a OR (95% CI) b P Ca vs Co a OR (95% CI) b P / (ref) / (ref) / (ref) / ( ) 65/ ( ) 84/ ( ) 2 6/ ( ) 3/ ( ) 3/ ( ) Per copy variant allele d 0.68 ( ) ( ) ( ) 0.03 European American 0 580/ (ref) / (ref) / (ref) / ( ) 18/ ( ) 14/ ( ) 2 1/ ( ) 0/5 1/ ( ) Per copy variant allele d 0.56 ( ) ( ) ( ) 0.06 African American 0 447/ (ref) / (ref) / (ref) / ( ) 47/ ( ) 70/ ( ) 2 5/ ( ) 3/ ( ) 2/ ( ) Per copy variant allele d 0.69 ( ) ( ) ( ) 0.06 a Ca, Cases; Co, Controls b OR, odds ratios; 95% CI, 95% confidence intervals c Variables adjusted in the unconditional logistic regression model are age (continuous), proportion of european ancestry (continous), education (less than 12th grade, high school, some college, college, post- graduate), family history of breast cancer (yes/no), smoking status (current, former, never), parity (nulliparous, 1, 2, 3, 4, 5+), HRT use (yes/no), and study site (New York, New Jersey). For pre- and post- menopausal women combined, menopausal status was also included in the model (premenopausal/postmenopausal). For analyses combining EA and AA women together, self- reported race was also included in the model (EA, AA). d Per copy variant allele p- value (p- trend) determined by coding genotypes as having 0, 1, or 2 variant allele, which were analyzed as an ordinal variable.

10 Table S3: 2q35 encnv Genotype and Overall Breast Cancer by ER Status in WCHS c Genotype ER+ ER- ER- vs ER+ Ca vs Co a OR (95% CI) b P Ca vs Co a OR (95% CI) b P Ca vs Co a OR (95% CI) b P All Women 0 581/ (ref) / (ref) / (ref) / ( ) 37/ ( ) 37/ ( ) 2 3/ ( ) 1/ ( ) 1/ ( ) Per copy variant allele d 0.74 ( ) ( ) ( ) 0.70 European American 0 354/ (ref) / (ref) / (ref) / ( ) 7/ ( ) 7/ ( ) 2 1/ ( ) 0/7 0/1 Per copy variant allele d 0.58 ( ) ( ) ( ) 0.15 African American 0 227/ (ref) / (ref) / (ref) / ( ) 30/ ( ) 30/ ( ) 2 2/ ( ) 1/ ( ) 1/ ( ) Per copy variant allele d 0.76 ( ) ( ) ( ) 0.92 a Ca, Cases; Co, Controls b OR, odds ratios; 95% CI, 95% confidence intervals c Variables adjusted in the unconditional logistic regression model are age (continuous), menopausal status (pre, post), proportion of european ancestry (continous), education (less than 12th grade, high school, some college, college, post- graduate), family history of breast cancer (yes/no), smoking status (current, former, never), parity (nulliparous, 1, 2, 3, 4, 5+), HRT use (yes/no), and study site (New York, New Jersey). For analyses combining EA and AA women together, self- reported race was also included in the model (EA, AA). d Per copy variant allele p- value (p- trend) determined by coding genotypes as having 0, 1, or 2 variant allele, which were analyzed as an ordinal variable.

11 Table S4: Association of imputed 2q35 encnv genotype and linked variants with breast cancer risk overall and by estrogen receptor status in icogs. Overall ER- positive ER- negative SNP Position Ref Alt r 2 MAF OR (95%CI) P OR (95%CI) P OR (95%CI) P rs C A ( ) 5.6x10-17 ( ) 3.6x10-14 ( ) 0.16 rs A C ( ) 6.6x10-17 ( ) 1.4x10-14 ( ) 0.21 rs C T ( ) 7.2x10-17 ( ) 1.7x10-14 ( ) 0.2 rs G A ( ) 1.1x10-16 ( ) 1.9x10-14 ( ) 0.21 rs C G ( ) 1.4x10-16 ( ) 6.0x10-14 ( ) 0.21 rs T G ( ) 2.2x10-16 ( ) 1.8x10-13 ( ) 0.22 chr2: :d GAAT G ( ) 2.8x10-16 ( ) 2.0x10-13 ( ) 0.07 rs T A ( ) 2.8x10-16 ( ) 2.0x10-13 ( ) 0.07 chr d TAATA T ( ) 3.3x10-16 ( ) 2.1x10-13 ( ) 0.07 rs A G ( ) 3.7x10-16 ( ) 2.2x10-13 ( ) q35 encnv * T ( ) 6.9x10-16 ( ) 3.1x10-13 ( ) 0.09 chr i A AT ( ) 8.7x10-16 ( ) 4.7x10-13 ( ) 0.08 rs G T ( ) 1.8x10-15 ( ) 6.8x10-13 ( ) 0.09 chr d GA G ( ) 3.2x10-15 ( ) 2.9x10-12 ( ) 0.07

12 Table S5: Conditional analysis of 2q35 encnv with previously reported loci Variant Position (chr2; hg19) Conditional OR(95%CI) Conditional P- value rs ,920, ( ) 4.74x q35 encnv 217,955, ( ) 1.25x10-14 rs ,296, ( ) 4.98x10-15

13 Table S6: Primer sequences used in experiments Assay Name Experiment Forward Reverse IGFBP5 3'UTR Expression TGACAACTGTGCTATCCATGTGGG ATTTCACAGACTCTGGCCTCCTCT hactin Expression CCTTAATGTCACGCACGATTTCC GAGAAGATGACCCAGATCATGTTT rs pre- amp Pre- amplification CCAGTACCTCGATTCTGCTCTA GGACTAAATGGCCTACGGAAAG rs A Allelic Expression TCTAGTAACACAGGCCTCAC CCAGTCCCTCCATAAGACTT rs C Allelic Expression " CCAGTCCCTCCATAAGACTG rs both Allelic Expression " CTCCAGTCCCTCCATAAGAC encnv wildtype Allelic ChIP AAAGCTCTTCTAAGTTCCTTGT CCCTTGTTTCCTCAATCACTG encnv deleted Allelic ChIP CTGAGTCTTGGTATAGTCAGGC " encnv both Allelic ChIP GGGAACAGTGATTGAGGAAA GTGACAGATCACTTCCTTCTT 217,560,272 3C - - Anchor TGAGAGTGGTGAGAGTGACACAGA ,560,655 3C " CAACTGGATATACCGTGCCCAAGA 217,580,365 3C " ATTTCAGATCGCTGTCCTGCACTC 217,640,855 3C " AACTTGGAGCATCCCTGAGGTTTC 217,721,284 3C " GGCTACCATTCCTTCACAACCTGT 217,798,338 3C " ACACGGTAGAGTGTGGGACTGTTA 217,848,589 3C " AACAGCAGAAAGGGTGGGAATGAG 217,938,485 3C " TTGAAAACGGCTCTAGACTCTGGAC 217,943,319 3C " TTGGCAGAGGTTGGAGCTTTGTAG 217,955,203 3C " TCCTTCCACTTCACCCTACAAAAC 217,966,314 3C " CCACCAGTTTGCCGTCTCCATTATA 217,971,957 3C " AGTCGCCTGTACAGAACATGTAGC 217,979,818 3C " TCCCTTCCTTGAGGATAGCAGAGA encnv wildtype AFLA Genotype /56FAM/TCCTCACCTATGTTTGTGCTT TAGACACTGCAGAGAGGGTCAAGT encnv variant AFLA Genotype " CCCTTGTTTCCTCAATCACTGTTCCC