Variant report

Variant	rs518632
Chromosome Location	chr4:74758477-74758478
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10007826	0.92[ASN][1000 genomes]
rs1366946	0.92[ASN][1000 genomes]
rs1366949	0.92[ASN][1000 genomes]
rs16850137	1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs2115691	0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2145615	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2367291	0.83[YRI][hapmap]
rs2367293	0.92[ASN][1000 genomes]
rs24772	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28404022	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2886927	0.91[YRI][hapmap]
rs2886969	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2886970	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2968710	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3097409	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3097411	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap]
rs3097412	0.91[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3111694	0.91[YRI][hapmap]
rs3111697	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3111698	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3117597	0.83[YRI][hapmap]
rs3117598	0.91[YRI][hapmap]
rs3117600	0.83[YRI][hapmap]
rs3117604	0.83[YRI][hapmap]
rs4074	0.86[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs482239	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493091	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs508977	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512606	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516224	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs519565	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537373	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541923	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548068	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551744	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561454	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs562213	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs569390	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573878	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593641	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596352	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623659	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634304	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs638767	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs654871	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655328	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs673038	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs680044	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs680452	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs683671	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684080	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6858086	0.91[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs7692638	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9991272	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv432612	chr4:74723372-74774372	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs518632	SEPT11	cis	parietal	SCAN
rs518632	G3BP2	cis	parietal	SCAN
rs518632	FAM47E	cis	parietal	SCAN
rs518632	CXCL6	cis	parietal	SCAN
rs518632	THOC1	trans	parietal	SCAN
rs518632	NPFFR2	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74752000-74760600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:74756800-74758600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr4:74756800-74759200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:74757000-74758800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:74757000-74759000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr4:74757000-74759000	Enhancers	Fetal Intestine Small	intestine
7	chr4:74757000-74760000	Enhancers	Fetal Intestine Large	intestine
8	chr4:74757200-74760000	Weak transcription	Fetal Kidney	kidney
9	chr4:74757200-74770400	Enhancers	NHDF-Ad	bronchial
10	chr4:74757400-74758600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr4:74757400-74761000	Weak transcription	Stomach Mucosa	stomach
12	chr4:74757600-74760200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:74757600-74760600	Weak transcription	Pancreas	Pancrea
14	chr4:74757600-74761200	Weak transcription	Spleen	Spleen
15	chr4:74757800-74759800	Weak transcription	Fetal Stomach	stomach
16	chr4:74758000-74759600	Enhancers	A549	lung
17	chr4:74758200-74760200	Weak transcription	Adipose Nuclei	Adipose
18	chr4:74758200-74760800	Weak transcription	Osteobl	bone
19	chr4:74758400-74758800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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