Variant report

Variant	rs7587596
Chromosome Location	chr2:189361402-189361403
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10153688	1.00[ASW][hapmap];0.83[CHD][hapmap];0.92[LWK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10153871	0.88[EUR][1000 genomes]
rs10172178	0.85[EUR][1000 genomes]
rs10180000	1.00[JPT][hapmap]
rs10185750	1.00[ASW][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189197	1.00[JPT][hapmap]
rs10199260	1.00[JPT][hapmap]
rs10203054	0.85[EUR][1000 genomes]
rs10804021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10931353	1.00[CEU][hapmap]
rs10931357	1.00[CEU][hapmap]
rs10931363	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679949	1.00[CEU][hapmap]
rs11683909	1.00[CEU][hapmap]
rs11683969	1.00[CEU][hapmap]
rs11685238	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685643	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs11693105	1.00[CEU][hapmap]
rs11695177	1.00[CEU][hapmap]
rs11695316	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11902664	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151605	1.00[CEU][hapmap]
rs12463744	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12475894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12476413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12693497	1.00[JPT][hapmap]
rs12995727	1.00[JPT][hapmap]
rs12997039	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032231	1.00[JPT][hapmap]
rs13386581	0.88[EUR][1000 genomes]
rs13386959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13393057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs13393442	1.00[CEU][hapmap]
rs13396968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs13397653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13412448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs13413644	0.85[EUR][1000 genomes]
rs13414327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13418031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13424809	0.85[EUR][1000 genomes]
rs1354902	1.00[JPT][hapmap]
rs1354904	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1354910	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1507551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1567184	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1807235	0.85[EUR][1000 genomes]
rs4128404	1.00[JPT][hapmap]
rs4453658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577225	0.85[EUR][1000 genomes]
rs4667219	1.00[JPT][hapmap]
rs4667220	1.00[JPT][hapmap]
rs4667229	1.00[JPT][hapmap]
rs4667231	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55663622	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61045757	0.85[EUR][1000 genomes]
rs6414119	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434277	1.00[JPT][hapmap]
rs6434285	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434286	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66641143	0.89[EUR][1000 genomes]
rs6707212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6709557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720983	1.00[JPT][hapmap]
rs6722940	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6727633	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67425558	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6744275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7419798	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7420808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7421510	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs7422739	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7423329	1.00[CEU][hapmap]
rs7423554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7424421	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562160	1.00[CEU][hapmap]
rs7568147	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7571197	1.00[JPT][hapmap]
rs7571494	1.00[JPT][hapmap]
rs7579593	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs7582643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7600043	0.81[EUR][1000 genomes]
rs7602180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8273	1.00[CHB][hapmap]

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	nsv534341	chr2:189200405-189368467	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv584055	chr2:189266823-189493686	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv834489	chr2:189329027-189494224	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1003974	chr2:189331760-189827814	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv533110	chr2:189354436-189462552	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7587596	GUCA1C	trans	brain	seeQTL
rs7587596	LRTM1	trans	brain	seeQTL
rs7587596	SLC5A7	trans	brain	seeQTL
rs7587596	CRX	trans	brain	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189329200-189399000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:189334600-189367600	Weak transcription	Fetal Lung	lung
3	chr2:189344000-189370200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:189344200-189390400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:189353000-189366400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:189355800-189382400	Weak transcription	Gastric	stomach
7	chr2:189356000-189370800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:189356400-189370000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:189356400-189371200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:189356400-189373600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:189356800-189362600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:189356800-189371000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:189357000-189370000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr2:189357800-189371000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:189358800-189362400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:189358800-189369800	Weak transcription	Placenta	Placenta
17	chr2:189359000-189362400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:189359200-189382200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:189359600-189361800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:189359600-189363000	Enhancers	NHDF-Ad	bronchial
21	chr2:189359800-189362400	Enhancers	Hela-S3	cervix
22	chr2:189360000-189362800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:189360400-189361800	Enhancers	Muscle Satellite Cultured Cells	--
24	chr2:189360400-189362600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:189360400-189363000	Enhancers	Osteobl	bone
26	chr2:189360600-189361600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:189360600-189361600	Enhancers	NHLF	lung
28	chr2:189360600-189361800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:189360600-189361800	Enhancers	Ovary	ovary
30	chr2:189360800-189361600	Enhancers	HSMM	muscle
31	chr2:189360800-189361800	Enhancers	Aorta	Aorta
32	chr2:189361200-189362600	Weak transcription	NH-A	brain
33	chr2:189361200-189364200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr2:189361200-189366000	Weak transcription	HUVEC	blood vessel
35	chr2:189361400-189361600	Enhancers	Esophagus	oesophagus
36	chr2:189361400-189361600	Enhancers	Pancreas	Pancrea
37	chr2:189361400-189361800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:189361400-189361800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:189361400-189362400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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