Multiple selective sweeps of ancient polymorphisms in and around LTα located in the MHC class III region on chromosome 6

Table 3 The effect of allelic variation on transcription factor binding affinity

Genomic coordinate	rs identifier	Reference allele	Alternate allele	Genic region	Transcription factor	Selection status	MAF	ClinVar
31,532,814	rs2857709	A	G	intergenic	ELF-1	Yes	Common	No
31,533,718	rs4947326	A	G	intergenic	Zfx	Yes	Common	No
31,533,722	rs113019108	C	T	intergenic	Zfx	No	Common	No
31,533,728	rs4947327	G	A	intergenic	Zfx	Yes	Common	No
31,534,206	rs2844485	A	G	intergenic	Nr1h3/Rxra	No	Common	No
31,535,455	rs549446426	G	A	intergenic	Arnt/Ahr, EGR2	No	Common	No
31,535,459	rs62395772	G	A	intergenic	Arnt/Ahr, EGR2	No	Common	No
31,535,462	rs538596719	T	C	intergenic	Arnt/Ahr, EGR2	No	Common	No
31,536,796	rs2844483	T	G	intergenic	FOXI1, Foxd3	No	Common	No
31,537,221	rs62395778	G	A	intergenic	IRF1, ZNF263	No	Common	No
31,540,313	rs909253	A	G	intronic	SPIB	No	Common	Yes
31,540,693	rs3093542	G	C	intronic	ZNF263	Yes	Common	No
31,541,848	rs3093547	T	A	non-coding exon/UTR	ARID3A, Prrx2	No	Common	No

SNP2TFBS [55] was used to map variants to known transcription factor binding sites (TFBSs) in the human genome. In the Table, we have listed the genomic coordinate (from build GRCh 37) of each polymorphic site along with the rs identifier, Reference/Alternate alleles, the genic region in which each site is located, as well as the corresponding transcription factor that binds to the TFBSs where polymorphisms occurred. Furthermore, we indicated whether or not a given polymorphic site was inferred to be under selection (Yes/No) and if alleles at this site were common (based on minor allele frequency [MAF]). We also determined if variants were previously reported in the ClinVar database (Yes/No) [57]

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