SupplementaryTable 1 PCR primers for amplifying SNP-containing fragments from human genomic DNA

SNP / Sense primer / Antisense primer / DNA size
rs2615787A / CGGGGTACCCACTTTAACTCTTACTCCTAGAAAATTC / GAAGATCTCTCCTGAGTTAAGCAAGTACACGTAG / 117bp
rs2615787C / CGGGGTACCCACTTTAACTCTTACTCCTAGACAATTC
rs2738081C / CGGGGTACCGTCCAGTGTGAGCCCCTCATATTTAC / GAAGATCTAACAGTGACCACCTGCTAAGAGT / 129bp
rs2738081A / CGGGGTACCGTCCAGTGTGAGACCCTCATATTTAC
rs2738048T / CGGGGTACCCGTTTTTTGGCACCAATGACAGTTG / GAAGATCTCTAACTAATGCCTGATGATACGAG / 110bp
rs2738048C / CGGGGTACCCGTTTTTTGGCACCAACGACAGTTG
rs4288398A / CGGGGTACCCGGGGCAGAATAACCTTGTTAATG / GAAGATCTCAACTATGAAGCTCCCCATCCCTGAC / 106bp
rs4288398G / CGGGGTACCCGGGGCAGAATAGCCTTGTTAATG
rs6984215T / CGGGGTACCGAAAGTACAGATTTATTGACACAC / GAAGATCTGGAGAATAGGGAAATAGGATAATC / 125bp
rs6984215C / CGGGGTACCGAAAGTACAGATTTACTGACACAC

Sequences in italic donate sites of restriction enzymeKpnI and BglII. The SNP allele is marked underline.

SupplementaryTable 2 Oligonucleotides representing the putative TFBS used for electrophoretic mobility shift assay

PolymorphismSNP / Allele / Ssense / Aantisense
rs2738081 / C / 5’CCAGTGTGAGCCCCTCATATTTAC 3’ / 5’GTAAATATGAGGGGCTCACACTGG 3’
rs2738081 / A / 5’CCAGTGTGAGACCCTCATATTTAC 3’ / 5’GTAAATATGAGGGTCTCACACTGG 3’
rs2738048 / C / 5’ TTTGGCACCAACGACAGTTGTAAG 3’ / 5’ CTTACAACTGTCGTTGGTGCCAAA 3’
rs2738048 / T / 5’ TTTGGCACCAATGACAGTTGTAAG 3’ / 5’ CTTACAACTGTCATTGGTGCCAAA 3’
rs6984215 / C / 5’ GTACAGATTTACTGACACAC 3’ / 5’ GTGTGTCAGTAAATCTGTAC 3’
rs6984215 / A / 5’ GTACAGATTTATTGACACAC 3’ / 5’ GTGTGTCAATAAATCTGTAC 3’
rs2615787 / A / 5’ TACTCCTAGAAAATTCTTTAGCC 3’ / 5’ GGCTAAAGAATTTTCTAGGAGTA 3’
rs2615787 / C / 5’ TACTCCTAGACAATTCTTTAGCC 3’ / 5’ GGCTAAAGAATTGTCTAGGAGTA 3’

Nucleotides representing the polymorphisms are underlined.

Supplementary Table 3The allele frequencies of the 7 associated SNPs in selected HapMap reference populations

SNP / Position / Allele / Allele frequencya
CHBb / JPTb / CEUb / YRIb
rs2615787 / 6811149 / C / 0.3 / 0.38 / 0.44 / N
rs2738081 / 6815518 / A / 0.14 / 0.15 / 0.15 / 0.11
rs2738058 / 6821617 / G / 0.29 / 0.41 / 0.6 / 0.65
rs2738048 / 6822785 / C / 0.3 / 0.42 / 0.29 / 0.18
rs4288398 / 6881638 / A / 0.29 / 0.35 / 0.32 / 0.08
rs6984215 / 6884878 / C / 0.33 / 0.32 / 0.37 / 0.04
rs12716641 / 6898998 / C / 0.2 / 0.22 / 0.42 / 0.24

aAllelic frequency information based on HapMap Data Release 28 (phase II+III); only founder genotypes included in the analysis.

bPopulation descriptors: JPT: Japanese in Tokyo, Japan (N=45). CHB: Han Chinese in Beijing, China (N=45). CEU: Utah residents with Northern and Western European ancestry from the CEPH collection (N=60). YRI: Yoruban in Ibadan, Nigeria (N=60).

Supplementary Figure 1

EMSAs performed with biotin-labeled rs2615787oligonucleotide and nuclear extracts prepared from HEK293T cells transfected with an expression plasmid-encoding HSTF (H). Specific binding of nuclear protein to the respective oligonucleotide was tested by adding increasing concentration of unlabeled oligonucleotide probe.There was no detectable band corresponding to shifted complex when rs2615787oligonucleotide interacted with nuclear proteins. Lanes 1 and 6, no nuclear extracts; lanes 2 and 7, 10ug nuclear extracts with 20 fmol biotin-label probe; lanes 3 and 8,complexwas included unlabeled competitor in 200-fold molar excess; lanes 4 and 9, complexwas included unlabeled competitor in 400-fold molar excess; and lanes 5 and 10, nuclear extracts from HEk293T cells without transfection (M). I: free biotin-labeled probes.

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