Variant report

Variant	rs664228
Chromosome Location	chr5:41596142-41596143
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1027348	1.00[CHD][hapmap]
rs11740571	0.83[ASN][1000 genomes]
rs11741653	0.83[ASN][1000 genomes]
rs11742364	0.80[AFR][1000 genomes]
rs11748177	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1645010	0.83[ASN][1000 genomes]
rs16871562	0.83[ASN][1000 genomes]
rs16871673	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2172925	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs586373	0.83[ASN][1000 genomes]
rs589564	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs589757	0.83[ASN][1000 genomes]
rs59502841	0.83[ASN][1000 genomes]
rs597921	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs598318	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs599176	0.83[ASN][1000 genomes]
rs600137	0.83[ASN][1000 genomes]
rs600464	0.83[ASN][1000 genomes]
rs602538	0.83[ASN][1000 genomes]
rs603979	0.83[ASN][1000 genomes]
rs610657	0.83[ASN][1000 genomes]
rs621609	0.83[ASN][1000 genomes]
rs629883	0.83[ASN][1000 genomes]
rs631626	0.83[ASN][1000 genomes]
rs633282	0.83[ASN][1000 genomes]
rs633361	0.83[ASN][1000 genomes]
rs634858	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636459	0.83[ASN][1000 genomes]
rs637761	0.83[ASN][1000 genomes]
rs644461	0.83[ASN][1000 genomes]
rs645561	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs648014	0.83[ASN][1000 genomes]
rs650073	0.83[ASN][1000 genomes]
rs650160	0.83[ASN][1000 genomes]
rs651256	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs651888	0.83[ASN][1000 genomes]
rs652237	0.83[ASN][1000 genomes]
rs659547	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs660333	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs660833	0.83[ASN][1000 genomes]
rs661845	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662204	0.83[ASN][1000 genomes]
rs664202	0.83[ASN][1000 genomes]
rs664634	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665999	0.83[ASN][1000 genomes]
rs666457	0.85[AFR][1000 genomes]
rs669700	0.83[ASN][1000 genomes]
rs673538	0.83[ASN][1000 genomes]
rs674512	0.83[ASN][1000 genomes]
rs675146	1.00[CHB][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs675609	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs676512	1.00[CHD][hapmap]
rs676746	0.83[ASN][1000 genomes]
rs677170	0.83[ASN][1000 genomes]
rs677450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs677610	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677612	0.83[ASN][1000 genomes]
rs677997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678996	0.83[ASN][1000 genomes]
rs681400	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs681880	0.83[ASN][1000 genomes]
rs682701	0.83[ASN][1000 genomes]
rs682711	0.83[ASN][1000 genomes]
rs684130	0.83[ASN][1000 genomes]
rs6869561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6885560	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6888718	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881563	chr5:41560079-41616100	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv2753438	chr5:41571309-41600812	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv462124	chr5:41585079-41596269	Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
4	nsv597880	chr5:41585079-41596269	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	nsv881628	chr5:41585079-41600651	Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	esv3470450	chr5:41585589-41596580	ZNF genes & repeats Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	esv3470451	chr5:41585589-41596580	ZNF genes & repeats Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	nsv823059	chr5:41585612-41596478	Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	nsv524669	chr5:41586405-41596269	Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
10	nsv818349	chr5:41586405-41596269	Bivalent/Poised TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs664228	GDNF	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41588000-41596400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links