Variant report

Variant	rs17758599
Chromosome Location	chr8:50946702-50946703
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 160 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs1000638	0.81[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs1000639	0.81[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs10093604	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10095985	0.87[JPT][hapmap]
rs10096871	0.81[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs10098057	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.94[ASN][1000 genomes]
rs10504094	0.81[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs10504096	0.81[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs10504098	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[ASN][1000 genomes]
rs10957813	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10957814	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[ASN][1000 genomes]
rs10957828	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11775978	0.89[ASN][1000 genomes]
rs11778998	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11780070	0.90[ASN][1000 genomes]
rs11781981	0.87[ASN][1000 genomes]
rs11786703	0.87[ASN][1000 genomes]
rs11986160	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs11989367	0.84[ASN][1000 genomes]
rs11991940	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12542067	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[ASN][1000 genomes]
rs12543077	0.91[MEX][hapmap]
rs12544631	0.93[JPT][hapmap]
rs12544986	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12545263	0.86[ASN][1000 genomes]
rs13249415	0.93[JPT][hapmap]
rs13251587	0.93[JPT][hapmap]
rs13260265	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs13271983	0.87[ASN][1000 genomes]
rs13277538	0.90[ASN][1000 genomes]
rs13340639	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1450127	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1486471	0.82[MEX][hapmap]
rs149992	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16914250	0.86[JPT][hapmap]
rs16914346	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs16914376	0.90[ASN][1000 genomes]
rs16914459	0.87[ASN][1000 genomes]
rs1903311	0.81[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs1906070	0.86[JPT][hapmap]
rs203612	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs203616	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs203621	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs203623	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs203632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs203908	1.00[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs203925	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs203928	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203930	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs203932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs203933	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs203935	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs203936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs203937	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs203938	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs203939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs203940	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs203942	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs203945	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs203947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs203949	0.95[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs203951	0.94[EUR][1000 genomes]
rs203960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2084590	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2084591	0.88[ASN][1000 genomes]
rs2385812	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs34047312	0.86[ASN][1000 genomes]
rs34641787	0.86[ASN][1000 genomes]
rs34722367	0.90[ASN][1000 genomes]
rs34997857	0.87[ASN][1000 genomes]
rs35989044	0.90[ASN][1000 genomes]
rs36006902	0.90[ASN][1000 genomes]
rs420489	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4448283	0.81[ASN][1000 genomes]
rs4873126	0.87[ASN][1000 genomes]
rs4873127	0.87[ASN][1000 genomes]
rs4873128	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[ASN][1000 genomes]
rs4873129	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[ASN][1000 genomes]
rs4873131	0.88[ASN][1000 genomes]
rs4873132	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs4873133	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4873134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4873135	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs4873137	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4873405	0.90[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs4873406	0.81[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4873407	0.86[ASN][1000 genomes]
rs4873408	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[ASN][1000 genomes]
rs4873411	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4873412	0.89[ASN][1000 genomes]
rs4873413	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4873414	0.90[ASN][1000 genomes]
rs4873415	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4873416	0.90[ASN][1000 genomes]
rs4873417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4873418	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4873419	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4873420	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4873421	0.90[ASN][1000 genomes]
rs4873426	0.88[ASN][1000 genomes]
rs4873427	0.88[ASN][1000 genomes]
rs4873428	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs4873431	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs4873433	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs56007637	0.87[ASN][1000 genomes]
rs56725	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62515375	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62516672	0.89[ASN][1000 genomes]
rs62516685	0.90[ASN][1000 genomes]
rs62516687	0.90[ASN][1000 genomes]
rs6472947	0.91[ASN][1000 genomes]
rs6983498	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs6986896	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6988843	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[ASN][1000 genomes]
rs6991753	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6996646	0.81[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs6999722	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6999870	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7001686	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7002235	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[ASN][1000 genomes]
rs7004088	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7010037	0.90[ASN][1000 genomes]
rs7013247	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7013995	0.81[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs7016161	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[ASN][1000 genomes]
rs7018082	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs721441	0.81[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs7386487	0.92[ASN][1000 genomes]
rs7817040	0.88[ASN][1000 genomes]
rs7817638	0.88[ASN][1000 genomes]
rs7820951	0.87[ASN][1000 genomes]
rs7824938	0.87[ASN][1000 genomes]
rs7825053	0.87[ASN][1000 genomes]
rs7825063	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7835849	0.88[ASN][1000 genomes]
rs870754	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs884561	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs898520	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[ASN][1000 genomes]
rs9298278	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs9298279	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs987356	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353749	chr8:50530807-51139242	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv916392	chr8:50827638-51395140	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1022115	chr8:50864995-50981944	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv611311	chr8:50865230-50980320	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv34788	chr8:50873247-50965438	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3479183	chr8:50873277-50965062	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1033098	chr8:50873293-50965692	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv2757272	chr8:50873293-50968942	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv2759613	chr8:50873293-51137995	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv3479184	chr8:50873317-50965027	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv3479185	chr8:50873317-50965027	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv3692982	chr8:50875494-50959622	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv1023258	chr8:50877934-50964286	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv2758621	chr8:50886593-51137995	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv611312	chr8:50930075-51011122	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv890871	chr8:50936174-51040022	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv890872	chr8:50946702-51032813	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17758599	EFCAB1	cis	parietal	SCAN
rs17758599	SNTG1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:50945400-50952200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr8:50946000-50947000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr8:50946200-50946800	Enhancers	H1 Cell Line	embryonic stem cell
4	chr8:50946200-50947600	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr8:50946200-50947600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr8:50946200-50947800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr8:50946400-50947600	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr8:50946400-50947600	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr8:50946400-50947800	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr8:50946600-50947000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr8:50946600-50947600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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