Variant report

Variant	rs2366989
Chromosome Location	chr12:76018340-76018341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:76015495..76018360-chr12:76104509..76107219,2	MCF-7	breast:
2	chr12:76013741..76020372-chr12:76422912..76427305,12	MCF-7	breast:
3	chr12:76017499..76019528-chr12:76384312..76386033,2	MCF-7	breast:
4	chr12:76015734..76021626-chr12:76097256..76101818,9	MCF-7	breast:
5	chr12:76014354..76029119-chr12:76417641..76428409,36	MCF-7	breast:
6	chr12:76017185..76019394-chr12:76337259..76339909,2	MCF-7	breast:
7	chr12:76017340..76020194-chr12:76022357..76024091,3	MCF-7	breast:

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

Extended variants
information (count: 67 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10748282	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10748283	0.81[EUR][1000 genomes]
rs10785198	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10785199	0.81[EUR][1000 genomes]
rs10785200	0.81[EUR][1000 genomes]
rs10879929	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10879932	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10879933	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10879934	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10879935	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10879936	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10879937	0.81[EUR][1000 genomes]
rs10879938	0.89[CEU][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs10879945	0.81[CEU][hapmap]
rs10879949	0.88[ASN][1000 genomes]
rs11180562	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11180575	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11180584	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11180598	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11180603	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11495681	0.81[EUR][1000 genomes]
rs11514051	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11519910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11520226	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12811250	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1480005	0.81[EUR][1000 genomes]
rs17115238	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2054516	0.87[ASN][1000 genomes]
rs2054518	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2366988	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2886826	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2886828	0.82[ASN][1000 genomes]
rs34406885	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3847671	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3898937	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4323912	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4882631	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4882635	0.85[ASN][1000 genomes]
rs58886425	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60465677	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6582293	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6582294	0.90[ASN][1000 genomes]
rs7137366	0.81[CEU][hapmap]
rs7137610	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7297580	0.87[ASN][1000 genomes]
rs7300994	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7305673	0.89[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7314159	0.84[ASN][1000 genomes]
rs7314220	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7315474	0.90[ASN][1000 genomes]
rs733880	0.89[CEU][hapmap]
rs733881	0.89[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap]
rs7955264	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7956673	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7956953	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7958508	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7962144	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7962276	0.89[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7979460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7979600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7980713	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9634253	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]

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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs2366989	GLIPR1L1	cis	cerebellum	SCAN
rs2366989	GLIPR1L2	cis	lung	GTEx
rs2366989	GLIPR1L1	cis	lymphoblastoid	seeQTL
rs2366989	GLIPR1L2	cis	Artery Tibial	GTEx
rs2366989	KRR1	cis	parietal	SCAN
rs2366989	KRR1	cis	cerebellum	SCAN
rs2366989	GLIPR1L2	cis	Nerve Tibial	GTEx
rs2366989	GLIPR1L2	cis	Thyroid	GTEx
rs2366989	RP11-585P4.5	cis	Artery Tibial	GTEx
rs2366989	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs2366989	GLIPR1	cis	parietal	SCAN
rs2366989	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs2366989	GLIPR1	cis	cerebellum	SCAN
rs2366989	GLIPR1L2	cis	parietal	SCAN
rs2366989	GLIPR1L1	cis	multi-tissue	Pritchard
rs2366989	GLIPR1L2	cis	cerebellum	SCAN
rs2366989	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs2366989	GLIPR1L2	cis	Esophagus Muscularis	GTEx
rs2366989	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76015600-76018600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:76016200-76018400	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr12:76016400-76018400	Enhancers	NHEK	skin
4	chr12:76016400-76018600	Enhancers	Hela-S3	cervix
5	chr12:76016400-76018600	Enhancers	HepG2	liver
6	chr12:76016800-76020800	Weak transcription	K562	blood
7	chr12:76017400-76018400	Enhancers	A549	lung
8	chr12:76017400-76018800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:76017600-76018400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr12:76017600-76018400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr12:76017600-76018400	Enhancers	Fetal Intestine Small	intestine
12	chr12:76017600-76025200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:76017800-76018400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:76017800-76018400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:76017800-76021400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr12:76017800-76021400	Weak transcription	Pancreas	Pancrea
17	chr12:76017800-76022600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:76017800-76028800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:76018000-76018400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr12:76018000-76025400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:76018000-76025400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:76018000-76028600	Weak transcription	NHLF	lung
23	chr12:76018000-76028800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:76018200-76018400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr12:76018200-76029600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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