Variant report

Variant	rs11634271
Chromosome Location	chr15:50439682-50439683
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50437707..50440587-chr15:50443318..50445441,2	MCF-7	breast:
2	chr15:50433897..50436991-chr15:50437166..50439975,3	MCF-7	breast:
3	chr15:50436327..50442259-chr15:50645496..50648593,7	MCF-7	breast:
4	chr15:50436281..50440300-chr15:50607004..50610746,4	MCF-7	breast:
5	chr15:50438596..50441620-chr15:50472701..50475039,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000244879	Chromatin interaction
ENSG00000140284	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000104043	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10519250	1.00[ASW][hapmap]
rs10519262	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11070751	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11070752	0.89[GIH][hapmap]
rs11070753	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11632133	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11637647	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12439182	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12443171	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12593937	1.00[ASW][hapmap]
rs12901981	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12904370	0.86[CEU][hapmap];0.85[GIH][hapmap]
rs12915230	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12915287	1.00[ASW][hapmap];0.84[GIH][hapmap]
rs12915987	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2413992	1.00[ASW][hapmap]
rs2414025	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34146758	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4775865	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5026421	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67251119	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7171888	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7176805	0.82[CEU][hapmap]
rs7402755	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8027073	1.00[ASW][hapmap]
rs8041124	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs933854	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv904208	chr15:50428495-50457858	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11634271	ATP8B4	cis	multi-tissue	Pritchard
rs11634271	ATP8B4	cis	parietal	SCAN
rs11634271	SCG3	cis	parietal	SCAN
rs11634271	SLC27A2	cis	parietal	SCAN
rs11634271	TNFAIP8L3	cis	cerebellum	SCAN
rs11634271	ATP8B4	cis	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50430600-50442600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:50437800-50441200	Weak transcription	HMEC	breast
3	chr15:50437800-50441200	Weak transcription	NHEK	skin
4	chr15:50439000-50441400	Weak transcription	NHDF-Ad	bronchial
5	chr15:50439200-50441200	Weak transcription	Hela-S3	cervix
6	chr15:50439200-50441200	Weak transcription	K562	blood
7	chr15:50439400-50439800	Weak transcription	A549	lung
8	chr15:50439400-50440600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:50439400-50440800	Enhancers	Liver	Liver

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