Variant report

Variant	rs4620204
Chromosome Location	chr7:102594217-102594218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10228495	0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs10241865	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10242028	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10250490	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10271157	0.90[ASN][1000 genomes]
rs10271184	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10273725	0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10279449	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap]
rs10808120	0.82[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap]
rs1100046	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11514917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11972261	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs11976237	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs11978799	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11981980	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs12537977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12666317	0.82[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap]
rs12668434	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs13232194	0.95[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs13233521	0.91[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];0.84[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13242493	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1541519	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap]
rs1608651	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs17136090	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs1829957	0.81[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2190673	0.90[ASN][1000 genomes]
rs2228686	0.86[ASN][1000 genomes]
rs2411059	0.96[ASN][1000 genomes]
rs28856331	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41501847	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4296965	0.96[ASN][1000 genomes]
rs4609128	0.82[ASN][1000 genomes]
rs4729860	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs4729873	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap]
rs56269620	0.83[ASN][1000 genomes]
rs6465876	1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.84[ASN][1000 genomes]
rs6465878	0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6465880	0.90[ASN][1000 genomes]
rs6945997	0.86[ASN][1000 genomes]
rs6946773	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs6947403	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6953980	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6960428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6969054	0.81[JPT][hapmap]
rs6978630	0.89[CHB][hapmap];0.91[JPT][hapmap]
rs7458786	0.81[ASN][1000 genomes]
rs7778418	0.95[CHD][hapmap];0.81[JPT][hapmap]
rs7779145	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs7780405	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs7780981	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs7782908	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7785272	0.82[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap]
rs7789252	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7794668	0.92[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.98[MKK][hapmap];0.86[ASN][1000 genomes]
rs7800548	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7807055	0.82[ASN][1000 genomes]
rs847646	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs847647	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs847648	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs847649	0.83[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];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs847656	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs847658	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs865865	0.88[ASN][1000 genomes]
rs869332	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs955992	0.89[ASN][1000 genomes]
rs9718453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv464667	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv608060	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4620204	DPY19L2P2	cis	parietal	SCAN
rs4620204	CUX1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102574600-102594400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:102591000-102619400	Weak transcription	HSMM	muscle
3	chr7:102592600-102595200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr7:102594000-102603800	Weak transcription	K562	blood
5	chr7:102594200-102594600	Enhancers	Monocytes-CD14+_RO01746	blood

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