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Table S1 References Suggesting Involvement of Candidate Genes in Anorectal Malformations.

Table S2 Odds Ratios and 95% Confidence Intervals for Associations between SNPs in Candidate Genes and Anorectal Atresia.

Table S3 Linkage Disequilibrium Patterns and Proximity to other Coding Variants for SNPs Associated with Anorectal Atresia.

Figure S1 Association between GLI2 gene expression and GLI2 rs3738880 genotypes in lymphoblastoid cell lines from HapMap populations (CEU, Utah residents with Northern and Western European ancestry; CHB, Han Chinese in Beijing, China; GIH, Gujarati Indians in Houston, Texas; JPT, Japanese in Tokyo, Japan; LWK, Luhya in Webuye, Kenya; MEX, Mexican ancestry in Los Angeles, California; MKK, Maasai in Kinyawa, Kenya; YRI, Yoruban in Ibadan, Nigeria). Permutation (n = 10,000) was used to generate adjusted P values (padj).

Figure S2 Association between GLI2 gene expression and GLI2 rs3738880 genotypes in adipose tissue (F), lymphoblastoid cell lines (L), and skin samples (S) from healthy female twins of Caucasian ancestry. Twins from the same pair were analyzed independently (Twin1, Twin2). Permutation (n = 10,000) was used to generate adjusted P values (padj).

Figure S3 Association between HOXD12 gene expression and HOXD12 rs35817516 genotypes in lymphoblastoid cell lines from HapMap populations (CEU, Utah residents with Northern and Western European ancestry; GIH, Gujarati Indians in Houston, Texas; MEX, Mexican ancestry in Los Angeles, CA). Permutation (n = 10,000) was used to generate adjusted P values (padj).

Figure S4 Association between HOXD12 gene expression and HOXD12 rs35817516 genotypes in adipose tissue (F), lymphoblastoid cell lines (L), and skin samples (S) from healthy female twins of Caucasian ancestry. Twins from the same pair were analyzed independently (Twin1, Twin2). Permutation (n = 10,000) was used to generate adjusted P values (padj).

Figure S5 Association between PCSK5 gene expression and PCSK5 rs7040769 genotypes in lymphoblastoid cell lines from HapMap populations (CEU, Utah residents with Northern and Western European ancestry; LWK, Luhya in Webuye, Kenya; MEX, Mexican ancestry in Los Angeles, California; MKK, Maasai in Kinyawa, Kenya; YRI, Yoruban in Ibadan, Nigeria). Permutation (n = 10,000) was used to generate adjusted P values (padj).

Figure S6 Association between PCSK5 gene expression and PCSK5 rs2279659 genotypes in lymphoblastoid cell lines from HapMap populations (CEU, Utah residents with Northern and Western European ancestry; CHB, Han Chinese in Beijing, China; GIH, Gujarati Indians in Houston, Texas; JPT, Japanese in Tokyo, Japan; LWK, Luhya in Webuye, Kenya; MEX, Mexican ancestry in Los Angeles, California; MKK, Maasai in Kinyawa, Kenya; YRI, Yoruban in Ibadan, Nigeria). Permutation (n = 10,000) was used to generate adjusted P values (padj).

Figure S7 Association between PCSK5 gene expression and PCSK5 rs2279659 genotypes in fibroblasts (F), lymphoblastoid cell lines (L), and T-cells (T) from umbilical cord tissue and blood from newborns with Western European ancestry. Permutation (n = 10,000) was used to generate adjusted P values (padj).

Figure S8 Association between PCSK5 gene expression and PCSK5 rs2279659 genotypes in adipose tissue (F), lymphoblastoid cell lines (L), and skin samples (S) from healthy female twins of Caucasian ancestry. Twins from the same pair were analyzed independently (Twin1, Twin2). Permutation (n = 10,000) was used to generate adjusted P values (padj).

Figure S9 Association between BMP4 gene expression (measured using probe ILMN_1693749) and BMP4 rs17563 genotypes in lymphoblastoid cell lines from HapMap populations (CEU, Utah residents with Northern and Western European ancestry; CHB, Han Chinese in Beijing, China; GIH, Gujarati Indians in Houston, Texas; JPT, Japanese in Tokyo, Japan; LWK, Luhya in Webuye, Kenya; MEX, Mexican ancestry in Los Angeles, California; MKK, Maasai in Kinyawa, Kenya; YRI, Yoruban in Ibadan, Nigeria). Permutation (n = 10,000) was used to generate adjusted P values (padj).

Figure S10 Association between BMP4 gene expression (measured using probe ILMN_1740900) and BMP4 rs17563 genotypes in lymphoblastoid cell lines from HapMap populations (CEU, Utah residents with Northern and Western European ancestry; CHB, Han Chinese in Beijing, China; GIH, Gujarati Indians in Houston, Texas; JPT, Japanese in Tokyo, Japan; LWK, Luhya in Webuye, Kenya; MEX, Mexican ancestry in Los Angeles, California; MKK, Maasai in Kinyawa, Kenya; YRI, Yoruban in Ibadan, Nigeria). Permutation (n = 10,000) was used to generate adjusted P values (padj).

Figure S11 Association between BMP4 gene expression (measured using probe ILMN_1709734) and BMP4 rs17563 genotypes in lymphoblastoid cell lines from HapMap populations (CEU, Utah residents with Northern and Western European ancestry; CHB, Han Chinese in Beijing, China; GIH, Gujarati Indians in Houston, Texas; JPT, Japanese in Tokyo, Japan; LWK, Luhya in Webuye, Kenya; MEX, Mexican ancestry in Los Angeles, California; MKK, Maasai in Kinyawa, Kenya; YRI, Yoruban in Ibadan, Nigeria). Permutation (n = 10,000) was used to generate adjusted P values (padj).

Figure S12 Association between BMP4 gene expression (measured using probe ILMN_1693749) and BMP4 rs17563 genotypes in adipose tissue (F), lymphoblastoid cell lines (L), and skin samples (S) from healthy female twins of Caucasian ancestry. Twins from the same pair were analyzed independently (Twin1, Twin2). Permutation (n = 10,000) was used to generate adjusted P values (padj).

Figure S13 Association between BMP4 gene expression (measured using probe ILMN_1740900) and BMP4 rs17563 genotypes in adipose tissue (F), lymphoblastoid cell lines (L), and skin samples (S) from healthy female twins of Caucasian ancestry. Twins from the same pair were analyzed independently (Twin1, Twin2). Permutation (n = 10,000) was used to generate adjusted P values (padj).

Figure S14 Association between BMP4 gene expression (measured using probe ILMN_1709734) and BMP4 rs17563 genotypes in adipose tissue (F), lymphoblastoid cell lines (L), and skin samples (S) from healthy female twins of Caucasian ancestry. Twins from the same pair were analyzed independently (Twin1, Twin2). Permutation (n = 10,000) was used to generate adjusted P values (padj).

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