Variant report

Variant	rs3813565
Chromosome Location	chr15:79019610-79019611
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	chr15:79018937-79019720	HEK293	kidney:	n/a	chr15:79019379-79019395 chr15:79019383-79019392 chr15:79019647-79019656 chr15:79019379-79019395 chr15:79019648-79019658 chr15:79019380-79019394
9	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
10	TAF1	chr15:79019206-79019696	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr15:79019395-79019625	HCT-116	colon:	n/a	n/a
12	POLR2A	chr15:79019310-79019628	H1-hESC	embryonic stem cell:	n/a	n/a
13	TCF7L2	chr15:79019206-79019629	HCT-116	colon:	n/a	chr15:79019379-79019395 chr15:79019383-79019392 chr15:79019379-79019395 chr15:79019380-79019394
14	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
15	POLR2A	chr15:79019337-79019642	Hela-S3	cervix:	n/a	n/a
16	TBP	chr15:79019317-79019705	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr15:79019306-79019712	MCF-7	breast:	n/a	n/a
18	POLR2A	chr15:79019346-79019646	H1-hESC	embryonic stem cell:	n/a	n/a
19	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: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1021071	0.82[EUR][1000 genomes]
rs11072785	0.82[EUR][1000 genomes]
rs11072790	0.86[EUR][1000 genomes]
rs11072791	0.88[EUR][1000 genomes]
rs11072792	0.83[EUR][1000 genomes]
rs11629637	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11634543	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11638372	0.84[EUR][1000 genomes]
rs11638490	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11638830	0.92[CEU][hapmap]
rs11639049	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639166	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639181	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639347	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639372	0.81[EUR][1000 genomes]
rs11639375	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639382	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12286	0.92[CEU][hapmap]
rs12899135	0.92[CEU][hapmap]
rs12900168	0.83[CEU][hapmap]
rs12901913	0.86[EUR][1000 genomes]
rs12902602	0.82[EUR][1000 genomes]
rs12910627	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs1809420	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs1825082	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1825083	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996371	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap]
rs2869554	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2869566	0.88[EUR][1000 genomes]
rs34225855	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34563625	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35583595	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813564	0.91[ASN][1000 genomes]
rs3894347	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886579	0.83[EUR][1000 genomes]
rs4886580	0.83[EUR][1000 genomes]
rs4886581	0.87[ASN][1000 genomes]
rs4886582	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886583	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886584	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886586	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4886587	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4887077	0.86[EUR][1000 genomes]
rs4887082	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs4887086	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4887087	0.88[EUR][1000 genomes]
rs4887088	0.83[ASN][1000 genomes]
rs60191003	0.89[ASN][1000 genomes]
rs71448817	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7174367	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs72743199	0.85[EUR][1000 genomes]
rs922692	0.86[EUR][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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3813565	CHRNA5	cis	cerebellum	SCAN
rs3813565	ANKRD34C	cis	parietal	SCAN
rs3813565	PSMA4	cis	parietal	SCAN
rs3813565	CHRNA5	cis	parietal	SCAN

Chromatin state (count:17 , 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	chr15:79019400-79020200	Enhancers	H1 Cell Line	embryonic stem cell
3	chr15:79019400-79020200	Enhancers	Hela-S3	cervix
4	chr15:79019400-79020400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr15:79019400-79022000	Enhancers	A549	lung
6	chr15:79019600-79020000	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr15:79019600-79020000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:79019600-79020200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr15:79019600-79020200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:79019600-79020200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr15:79019600-79020200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:79019600-79020200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:79019600-79020400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:79019600-79020400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr15:79019600-79020400	Enhancers	Placenta Amnion	Placenta Amnion
16	chr15:79019600-79020800	Enhancers	NH-A	brain
17	chr15:79019600-79021400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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