Variant report

Variant	rs9634253
Chromosome Location	chr12:75925152-75925153
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75924261..75926963-chr12:76425587..76427776,2	MCF-7	breast:
2	chr12:75923805..75926647-chr12:76427379..76430609,3	MCF-7	breast:
3	chr12:75924745..75926908-chr12:75978244..75979819,2	MCF-7	breast:
4	chr12:75923131..75928282-chr12:76423369..76427377,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139289	Chromatin interaction
ENSG00000257453	Chromatin interaction
ENSG00000257839	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10748282	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10785198	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10879929	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10879932	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10879933	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10879934	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10879935	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10879936	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10879938	0.85[CEU][hapmap];0.91[GIH][hapmap]
rs11180562	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180575	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11180584	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11180598	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11180603	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11514051	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11519910	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11520226	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12811250	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1697759	0.80[EUR][1000 genomes]
rs17115238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2054518	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366988	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2366989	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2886826	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34406885	0.86[EUR][1000 genomes]
rs3847671	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3898937	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4323912	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4882631	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58886425	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60465677	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6582293	0.85[EUR][1000 genomes]
rs7137610	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs7300994	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7305673	0.85[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs7314220	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs733880	0.85[CEU][hapmap]
rs733881	0.85[CEU][hapmap];0.95[GIH][hapmap]
rs7955264	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7956673	0.84[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs7956953	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7958508	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7962144	0.85[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs7962276	0.85[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];0.81[TSI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7978312	1.00[LWK][hapmap]
rs7979460	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7979600	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7980713	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv428592	chr12:75766619-75936721	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv470305	chr12:75896688-75987360	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs9634253	RP11-585P4.5	cis	Esophagus Muscularis	GTEx
rs9634253	RP11-585P4.5	cis	Artery Tibial	GTEx
rs9634253	GLIPR1L2	cis	cerebellum	SCAN
rs9634253	GLIPR1L1	cis	lymphoblastoid	seeQTL
rs9634253	GLIPR1	cis	cerebellum	SCAN
rs9634253	GLIPR1L2	cis	parietal	SCAN
rs9634253	GLIPR1L2	cis	Nerve Tibial	GTEx
rs9634253	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs9634253	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs9634253	GLIPR1L2	cis	Muscle Skeletal	GTEx
rs9634253	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs9634253	KRR1	cis	parietal	SCAN
rs9634253	GLIPR1L2	cis	Artery Tibial	GTEx
rs9634253	GLIPR1	cis	parietal	SCAN
rs9634253	GLIPR1L1	cis	multi-tissue	Pritchard
rs9634253	GLIPR1L2	cis	lung	GTEx
rs9634253	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs9634253	KRR1	cis	cerebellum	SCAN
rs9634253	GLIPR1L2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75922800-75927200	Weak transcription	HSMMtube	muscle

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