Variant report

Variant	rs17115238
Chromosome Location	chr12:75939173-75939174
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:75933570..75936555-chr12:75937719..75939440,2	MCF-7	breast:
2	chr12:75938692..75940262-chr12:76423894..76425648,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257453	Chromatin interaction
ENSG00000139289	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10748282	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10785195	0.81[EUR][1000 genomes]
rs10785198	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10879929	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10879930	0.81[EUR][1000 genomes]
rs10879932	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10879933	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10879934	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10879935	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10879936	0.93[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10879938	0.85[CEU][hapmap]
rs11180562	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11180575	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11180584	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11180598	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11180603	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11514051	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11519910	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11520226	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12422952	0.80[CHB][hapmap]
rs12811250	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1697759	0.81[EUR][1000 genomes]
rs2054518	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2366988	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2366989	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2886826	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34406885	0.87[EUR][1000 genomes]
rs3847671	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3898937	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4323912	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4882631	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58886425	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60465677	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6582293	0.86[EUR][1000 genomes]
rs7137610	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs7300994	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7305673	0.86[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs7314220	0.93[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs733880	0.82[CEU][hapmap]
rs733881	0.85[CEU][hapmap]
rs7955264	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7956673	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs7956953	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7958508	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7962144	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs7962276	0.85[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs7966268	0.80[CHB][hapmap]
rs7979460	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7979600	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7980713	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9634253	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]

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	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	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
6	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs17115238	GLIPR1L2	cis	lung	GTEx
rs17115238	RP11-585P4.5	cis	Esophagus Muscularis	GTEx
rs17115238	GLIPR1L2	cis	Artery Tibial	GTEx
rs17115238	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs17115238	RP11-585P4.5	cis	Artery Tibial	GTEx
rs17115238	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs17115238	GLIPR1L2	cis	Thyroid	GTEx
rs17115238	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs17115238	GLIPR1L2	cis	Nerve Tibial	GTEx
rs17115238	RP11-585P4.5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75938000-75939200	Weak transcription	HSMMtube	muscle
2	chr12:75938600-75943600	Weak transcription	HUVEC	blood vessel
3	chr12:75938600-75947200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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