Variant report

Variant	rs2329772
Chromosome Location	chr7:40476625-40476626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10234636	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10245007	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10250287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10256791	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs10951634	0.92[CEU][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs11531505	1.00[ASN][1000 genomes]
rs11766930	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11772069	0.92[CEU][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap]
rs11980965	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12234460	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12531683	1.00[ASN][1000 genomes]
rs12532479	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs12533531	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12538229	0.97[ASN][1000 genomes]
rs12669577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12670267	0.96[ASN][1000 genomes]
rs12673516	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12701822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1319467	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16880229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17171680	0.92[CEU][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap]
rs17171683	0.85[JPT][hapmap]
rs17171686	0.88[CHD][hapmap];0.85[JPT][hapmap]
rs17171693	0.88[CHD][hapmap];0.85[JPT][hapmap]
rs17171694	0.88[CHD][hapmap];0.85[JPT][hapmap]
rs17171696	0.88[CHD][hapmap];0.85[JPT][hapmap]
rs17171703	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs17171704	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17171705	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs17171710	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2190261	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3890819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4143205	0.92[CEU][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap]
rs4379368	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4421260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap]
rs4434532	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4452702	0.92[CEU][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap]
rs4526265	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4563791	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4612243	0.85[CEU][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs4723954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs59682057	0.99[ASN][1000 genomes]
rs6462972	0.92[CEU][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap]
rs6462976	0.92[CEU][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap]
rs6945101	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs6965764	0.92[CEU][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs7782189	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7807217	0.92[CEU][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs9690724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030648	chr7:40218618-41032599	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv887985	chr7:40265510-40586674	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv817404	chr7:40295934-40573605	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv949540	chr7:40321357-40528147	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv34484	chr7:40383159-40489083	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv2757223	chr7:40384030-40497278	Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv2759526	chr7:40384030-40497278	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv8081	chr7:40393228-40486239	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv830969	chr7:40422576-40582389	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv1027075	chr7:40438478-40479723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
11	nsv1026022	chr7:40440560-40479066	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
12	esv2761320	chr7:40440560-40479723	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
13	nsv1032028	chr7:40440560-40479723	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
14	nsv1032883	chr7:40440560-40489083	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1019992	chr7:40443653-40479723	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
16	nsv1017615	chr7:40445480-40570791	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2329772	EPDR1	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40473600-40477000	Weak transcription	Psoas Muscle	Psoas
2	chr7:40475800-40479600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:40476000-40477000	Weak transcription	Ovary	ovary
4	chr7:40476000-40478000	Weak transcription	Aorta	Aorta
5	chr7:40476000-40478400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:40476000-40478400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr7:40476000-40478600	Enhancers	HSMMtube	muscle
8	chr7:40476000-40479600	Enhancers	NHDF-Ad	bronchial
9	chr7:40476200-40478200	Enhancers	Placenta Amnion	Placenta Amnion
10	chr7:40476200-40479000	Enhancers	HSMM	muscle
11	chr7:40476200-40479000	Enhancers	Osteobl	bone
12	chr7:40476400-40477400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr7:40476400-40478000	Enhancers	HUVEC	blood vessel
14	chr7:40476400-40478200	Enhancers	NHLF	lung
15	chr7:40476400-40478600	Enhancers	NH-A	brain
16	chr7:40476600-40477000	Enhancers	HepG2	liver
17	chr7:40476600-40477800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:40476600-40478000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:40476600-40478000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr7:40476600-40478000	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr7:40476600-40478200	Enhancers	HMEC	breast
22	chr7:40476600-40478200	Enhancers	NHEK	skin
23	chr7:40476600-40478600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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