Variant report

Variant	rs650653
Chromosome Location	chr7:124734582-124734583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1020629	0.94[CHB][hapmap];0.85[CHD][hapmap]
rs10247349	0.82[YRI][hapmap]
rs10256073	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap]
rs10266152	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs10269342	0.90[LWK][hapmap];0.96[YRI][hapmap]
rs1031952	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[ASN][1000 genomes]
rs10500102	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10954061	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs11761435	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs11767519	0.95[GIH][hapmap];0.81[JPT][hapmap]
rs11767649	0.81[YRI][hapmap]
rs11771004	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11771079	0.94[CHB][hapmap]
rs1248737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs12531213	0.90[ASN][1000 genomes]
rs12706627	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs13234634	0.96[YRI][hapmap]
rs1383749	0.83[ASW][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1404897	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs1471570	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs1481330	0.81[YRI][hapmap]
rs1481334	0.81[ASN][1000 genomes]
rs1525620	0.84[CHB][hapmap]
rs1552116	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1552117	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1568882	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17147723	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs17147889	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2291207	0.80[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap]
rs2929321	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2929322	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2929323	0.81[AFR][1000 genomes]
rs2968867	0.84[AFR][1000 genomes]
rs2968868	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34246481	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs585988	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs590516	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs598102	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612391	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs625037	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs627823	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651988	0.94[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs659269	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs663056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664062	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs669273	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs670910	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs671359	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6965957	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs6971179	0.82[YRI][hapmap]
rs7791488	0.82[YRI][hapmap]
rs7797011	0.94[CHB][hapmap]
rs967297	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs9785002	0.94[CHB][hapmap]
rs9942625	0.93[CHB][hapmap]

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	nsv429809	chr7:123937674-124835925	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv889139	chr7:124600505-124767295	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv3394090	chr7:124602150-124900799	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv464708	chr7:124703756-124805279	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv608344	chr7:124703756-124805279	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv831119	chr7:124714009-124890119	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs650653	POT1	cis	cerebellum	SCAN
rs650653	IMPDH1	cis	cerebellum	SCAN
rs650653	POT1	cis	parietal	SCAN
rs650653	FEZF1	cis	cerebellum	SCAN
rs650653	TMEM229A	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:124732200-124734600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:124734000-124734600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links