Variant report

Variant	rs899997
Chromosome Location	chr15:79019578-79019579
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr15:79019264-79019630	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAZ	chr15:79019109-79019631	K562	blood:	n/a	n/a
3	POLR2A	chr15:79019255-79019798	MCF-7	breast:	n/a	n/a
4	POLR2A	chr15:79019264-79019756	MCF-7	breast:	n/a	n/a
5	POLR2A	chr15:79019277-79019844	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr15:79019339-79019647	H1-hESC	embryonic stem cell:	n/a	n/a
7	TAF7	chr15:79019393-79019636	H1-hESC	embryonic stem cell:	n/a	n/a
8	TCF7L2	chr15:79019231-79019609	Hela-S3	cervix:	n/a	chr15:79019379-79019395 chr15:79019383-79019392 chr15:79019379-79019395 chr15:79019380-79019394
9	TCF7L2	chr15:79018937-79019720	HEK293	kidney:	n/a	chr15:79019379-79019395 chr15:79019383-79019392 chr15:79019647-79019656 chr15:79019379-79019395 chr15:79019648-79019658 chr15:79019380-79019394
10	TCF7L2	chr15:79019129-79019723	MCF-7	breast:	n/a	chr15:79019379-79019395 chr15:79019383-79019392 chr15:79019647-79019656 chr15:79019379-79019395 chr15:79019648-79019658 chr15:79019380-79019394
11	TAF1	chr15:79019206-79019696	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr15:79019395-79019625	HCT-116	colon:	n/a	n/a
13	POLR2A	chr15:79019310-79019628	H1-hESC	embryonic stem cell:	n/a	n/a
14	TCF7L2	chr15:79019206-79019629	HCT-116	colon:	n/a	chr15:79019379-79019395 chr15:79019383-79019392 chr15:79019379-79019395 chr15:79019380-79019394
15	TCF7L2	chr15:79019127-79019759	Hela-S3	cervix:	n/a	chr15:79019379-79019395 chr15:79019383-79019392 chr15:79019647-79019656 chr15:79019379-79019395 chr15:79019648-79019658 chr15:79019380-79019394
16	POLR2A	chr15:79019337-79019642	Hela-S3	cervix:	n/a	n/a
17	TBP	chr15:79019317-79019705	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr15:79019306-79019712	MCF-7	breast:	n/a	n/a
19	POLR2A	chr15:79019346-79019646	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr15:79019324-79019709	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:79010822..79012780-chr15:79019538..79021262,2	MCF-7	breast:
2	chr15:79018387..79019887-chr17:41464654..41467086,2	K562	blood:

Variant related genes	Relation type
ENSG00000261303	TF binding region
ENSG00000117971	Chromatin interaction
ENSG00000188825	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11072787	0.90[CEU][hapmap]
rs11072793	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11072794	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072799	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11629639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11629824	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11633170	0.94[ASW][hapmap];0.84[LWK][hapmap];0.96[MKK][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11633519	0.89[ASN][1000 genomes]
rs11634628	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11852887	0.89[EUR][1000 genomes]
rs11852909	0.93[EUR][1000 genomes]
rs11856441	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12899940	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12901228	0.91[EUR][1000 genomes]
rs12904489	0.81[EUR][1000 genomes]
rs12906977	0.82[EUR][1000 genomes]
rs12907178	0.83[ASN][1000 genomes]
rs12907207	0.83[EUR][1000 genomes]
rs12907432	0.83[EUR][1000 genomes]
rs12907511	0.88[ASN][1000 genomes]
rs12907536	0.82[EUR][1000 genomes]
rs12913779	0.83[EUR][1000 genomes]
rs1383634	0.92[EUR][1000 genomes]
rs1383635	0.92[EUR][1000 genomes]
rs1809412	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1809414	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1814880	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1825086	0.92[EUR][1000 genomes]
rs1904920	0.88[EUR][1000 genomes]
rs2017091	0.83[EUR][1000 genomes]
rs2219939	0.92[EUR][1000 genomes]
rs3971868	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4887074	0.85[CEU][hapmap]
rs4887078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4887085	0.90[ASN][1000 genomes]
rs4887091	0.95[CEU][hapmap]
rs71402966	0.82[EUR][1000 genomes]
rs7176070	0.83[ASN][1000 genomes]
rs7182567	0.95[CEU][hapmap];0.86[GIH][hapmap];0.84[TSI][hapmap]
rs755998	0.83[EUR][1000 genomes]
rs8030090	0.81[EUR][1000 genomes]
rs8030335	0.81[EUR][1000 genomes]
rs8043123	0.84[CEU][hapmap]
rs9888691	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv457208	chr15:78908032-79019610	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv570201	chr15:78908032-79019610	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv974606	chr15:78996783-79048337	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Coronary artery disease or large artery stroke	24262325	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs899997	RP11-650L12.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79019200-79020400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:79019400-79019600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr15:79019400-79020200	Enhancers	H1 Cell Line	embryonic stem cell
4	chr15:79019400-79020200	Enhancers	Hela-S3	cervix
5	chr15:79019400-79020400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr15:79019400-79022000	Enhancers	A549	lung

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