Variant report

Variant	rs4882637
Chromosome Location	chr12:76020864-76020865
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:76015734..76021626-chr12:76097256..76101818,9	MCF-7	breast:
2	chr12:76019796..76021718-chr12:76432029..76434118,2	MCF-7	breast:
3	chr12:76020325..76023301-chr12:76118678..76120430,2	MCF-7	breast:
4	chr12:76014354..76029119-chr12:76417641..76428409,36	MCF-7	breast:
5	chr12:76019985..76022320-chr12:76024831..76027786,2	MCF-7	breast:

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

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10748283	0.87[ASN][1000 genomes]
rs10748284	0.93[ASN][1000 genomes]
rs10785199	0.89[ASN][1000 genomes]
rs10785200	0.89[ASN][1000 genomes]
rs10879937	0.87[ASN][1000 genomes]
rs10879938	0.80[ASN][1000 genomes]
rs10879943	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10879944	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10879945	0.97[ASN][1000 genomes]
rs10879946	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10879947	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10879948	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11180600	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11180601	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11180605	0.93[ASN][1000 genomes]
rs11495681	0.86[ASN][1000 genomes]
rs12310185	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12318049	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1466464	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1480005	0.81[ASN][1000 genomes]
rs1871548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34767748	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34952545	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4882601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4882602	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4882639	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4882640	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7137366	0.92[ASN][1000 genomes]
rs7958075	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7958490	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7958760	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7972231	0.86[ASN][1000 genomes]
rs7973399	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7980645	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs899658	0.94[ASN][1000 genomes]
rs899659	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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4882637	GLIPR1L2	cis	Artery Tibial	GTEx
rs4882637	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs4882637	RP11-585P4.5	cis	Thyroid	GTEx
rs4882637	GLIPR1L2	cis	Thyroid	GTEx
rs4882637	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76017600-76025200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr12:76017800-76021400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr12:76017800-76021400	Weak transcription	Pancreas	Pancrea
4	chr12:76017800-76022600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:76017800-76028800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:76018000-76025400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:76018000-76025400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:76018000-76028600	Weak transcription	NHLF	lung
9	chr12:76018000-76028800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:76018200-76029600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:76018400-76022600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:76018400-76025000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:76018400-76025200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:76018400-76027600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr12:76018400-76029400	Weak transcription	NHEK	skin
16	chr12:76018600-76021800	Weak transcription	HepG2	liver
17	chr12:76018600-76024000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:76020800-76021000	Enhancers	K562	blood

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