Variant report

Variant	rs4886506
Chromosome Location	chr15:77207277-77207278
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77205286..77207679-chr15:77214041..77216350,2	K562	blood:
2	chr15:77200931..77204903-chr15:77206482..77209699,4	K562	blood:
3	chr15:77202308..77207759-chr15:77221259..77225491,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117906	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1011083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10851889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs10851892	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072619	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap]
rs11072625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs11072626	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11072631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11072632	0.82[CHB][hapmap]
rs11072636	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11072637	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11633869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap]
rs11634266	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11634428	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs11635584	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11637296	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11852395	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs11855296	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs11855534	0.95[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs12050866	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12439141	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12898416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12903331	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12903586	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12904149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12909065	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1443115	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1484990	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1567671	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2404600	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34450864	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35940181	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3764245	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3812908	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812909	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4312276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4886837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap]
rs4886840	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886842	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55817928	0.91[ASN][1000 genomes]
rs56275930	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6495224	0.88[ASN][1000 genomes]
rs71405231	0.80[ASN][1000 genomes]
rs7178250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8025991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs907593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs907594	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs920712	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs9635380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs9707794	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv1803942	chr15:77151005-77210457	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs4886506	SCAPER	cis	Adipose Subcutaneous	GTEx
rs4886506	ZNF291	cis	multi-tissue	Pritchard
rs4886506	SCAPER	cis	Esophagus Muscularis	GTEx
rs4886506	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs4886506	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs4886506	ZNF291	cis	lesional skin	skin_eQTL
rs4886506	SCAPER	cis	Esophagus Mucosa	GTEx
rs4886506	SCAPER	cis	cerebellum	SCAN
rs4886506	SCAPER	cis	multi-tissue	Pritchard
rs4886506	SCAPER	cis	Artery Tibial	GTEx
rs4886506	SCAPER	cis	parietal	SCAN
rs4886506	ISL2	cis	lymphoblastoid	seeQTL
rs4886506	SCAPER	cis	Nerve Tibial	GTEx
rs4886506	SCAPER	cis	Stomach	GTEx
rs4886506	ISL2	cis	Whole Blood	GTEx
rs4886506	NRG4	cis	parietal	SCAN
rs4886506	SCAPER	cis	lymphoblastoid	seeQTL
rs4886506	SCAPER	cis	lung	GTEx
rs4886506	SCAPER	cis	Whole Blood	GTEx
rs4886506	ZNF291	cis	uninvolved skin	skin_eQTL
rs4886506	SCAPER	cis	Skin Sun Exposed Lower leg	GTEx
rs4886506	SCAPER	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77203600-77209000	Enhancers	Placenta	Placenta

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