Variant report

Variant	rs2455308
Chromosome Location	chr5:40929513-40929514
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 152 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10035225	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10035592	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10035621	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10041257	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10041319	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10046046	0.92[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10051758	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10051888	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10054615	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10054948	0.95[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10056047	0.90[EUR][1000 genomes]
rs10056708	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10058274	0.95[CEU][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10059679	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10060965	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10063892	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10066847	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10072099	0.91[ASN][1000 genomes]
rs10072128	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10072214	0.98[ASN][1000 genomes]
rs10073246	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10076486	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10076663	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10077786	0.95[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10078706	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10079875	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10080165	0.95[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10472340	0.91[ASN][1000 genomes]
rs10472342	0.95[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10472344	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10473219	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10473220	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10473221	0.91[EUR][1000 genomes]
rs10473227	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10473228	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10941526	0.95[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10941527	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1120308	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739731	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11741315	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746650	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11748194	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12109051	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12110278	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12652909	0.91[ASN][1000 genomes]
rs12657195	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12658133	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12659571	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13353861	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13353862	0.81[ASN][1000 genomes]
rs13353865	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13354307	0.83[ASN][1000 genomes]
rs13354561	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13355045	0.83[ASN][1000 genomes]
rs13360188	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1393155	0.82[ASW][hapmap];0.95[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1393156	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1615402	0.89[CEU][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1645519	0.95[CEU][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16870407	0.92[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs16870425	0.95[CEU][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16870434	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs16870491	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1697939	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1697940	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1697941	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1697942	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1827363	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1827366	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1827367	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs188932	0.95[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2081153	0.95[CEU][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs225749	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2329430	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432155	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2455303	0.98[EUR][1000 genomes]
rs2455307	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];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2876848	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28770573	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831497	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28834109	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28860325	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28870511	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323555	0.82[EUR][1000 genomes]
rs323557	0.87[EUR][1000 genomes]
rs323558	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs323559	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs323563	0.82[EUR][1000 genomes]
rs323564	0.82[EUR][1000 genomes]
rs323566	0.95[CEU][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs34888872	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs369331	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs373411	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3792640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792642	0.90[CEU][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs4277953	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4277954	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439322	0.95[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs4461680	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs446920	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4559041	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567165	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs619491	0.82[ASW][hapmap];0.95[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62357063	0.98[EUR][1000 genomes]
rs62357601	0.85[EUR][1000 genomes]
rs62357603	0.82[EUR][1000 genomes]
rs62357605	0.82[EUR][1000 genomes]
rs62357612	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62357636	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62357641	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62358575	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62358580	0.98[EUR][1000 genomes]
rs72749504	0.83[ASN][1000 genomes]
rs72749508	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72749510	0.91[ASN][1000 genomes]
rs72749514	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72749521	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72749526	0.99[ASN][1000 genomes]
rs7445411	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7701643	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701662	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7701871	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704691	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7706776	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711745	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7716062	0.98[EUR][1000 genomes]
rs7717388	0.95[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7717391	0.95[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7717457	0.82[ASW][hapmap];0.95[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7717794	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7721703	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7724262	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7731772	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7731944	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7733440	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9292788	0.94[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9292790	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9292793	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9292794	0.99[ASN][1000 genomes]
rs9292795	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9292798	0.98[EUR][1000 genomes]
rs972007	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972008	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9885543	0.98[AFR][1000 genomes];0.96[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	nsv881467	chr5:40869802-41008650	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2757114	chr5:40874078-41009282	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759341	chr5:40874078-41009282	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv823055	chr5:40875708-41004839	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv35077	chr5:40875843-41000671	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv830268	chr5:40897361-41138366	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2455308	GDNF	cis	cerebellum	SCAN
rs2455308	OXCT1	cis	cerebellum	SCAN
rs2455308	RICTOR	cis	cerebellum	SCAN
rs2455308	DAB2	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40918000-40930800	Weak transcription	Fetal Heart	heart
2	chr5:40925800-40930600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr5:40926600-40936600	Weak transcription	Left Ventricle	heart
4	chr5:40928000-40931200	Strong transcription	Fetal Lung	lung
5	chr5:40929200-40929600	Enhancers	H9 Cell Line	embryonic stem cell
6	chr5:40929200-40929800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr5:40929200-40929800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr5:40929200-40929800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr5:40929200-40929800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr5:40929200-40929800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr5:40929200-40929800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr5:40929400-40933000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:40929400-40933000	Weak transcription	Ovary	ovary
14	chr5:40929400-40933200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links