Variant report

Variant	rs203940
Chromosome Location	chr8:50982597-50982598
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 189 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:182)

rs_ID	r²[population]
rs1000638	0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs1000639	0.90[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs10092399	0.81[MEX][hapmap]
rs10093604	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10094935	0.81[CHD][hapmap];0.93[JPT][hapmap]
rs10095985	0.87[JPT][hapmap]
rs10096871	0.90[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs10098057	0.90[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.92[ASN][1000 genomes]
rs10108468	0.85[CHD][hapmap]
rs10109835	0.88[JPT][hapmap]
rs10504094	0.90[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs10504096	0.90[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs10504098	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs10504099	0.93[JPT][hapmap]
rs10808817	0.93[JPT][hapmap]
rs10957813	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10957814	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[ASN][1000 genomes]
rs10957828	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10957853	0.92[JPT][hapmap]
rs11775978	0.92[ASN][1000 genomes]
rs11778998	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11780070	0.93[ASN][1000 genomes]
rs11781981	0.91[ASN][1000 genomes]
rs11786703	0.91[ASN][1000 genomes]
rs11986160	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs11989367	0.83[ASN][1000 genomes]
rs11991940	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12056425	0.93[JPT][hapmap]
rs12056426	0.93[JPT][hapmap]
rs12542067	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[ASN][1000 genomes]
rs12543077	0.91[MEX][hapmap]
rs12544631	0.93[JPT][hapmap]
rs12544986	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12545263	0.90[ASN][1000 genomes]
rs12545915	0.93[JPT][hapmap];0.82[MEX][hapmap]
rs12677964	0.85[JPT][hapmap]
rs12679356	0.85[JPT][hapmap]
rs12680748	0.93[JPT][hapmap]
rs13249415	0.93[JPT][hapmap]
rs13251587	0.93[JPT][hapmap]
rs13252320	0.92[JPT][hapmap]
rs13260265	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs13271983	0.91[ASN][1000 genomes]
rs13275607	0.84[JPT][hapmap]
rs13277538	0.93[ASN][1000 genomes]
rs13282956	0.93[JPT][hapmap]
rs13340639	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1349316	0.85[JPT][hapmap]
rs1349317	0.93[JPT][hapmap]
rs1450127	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1486471	0.82[MEX][hapmap]
rs149992	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs149994	0.81[AMR][1000 genomes]
rs1597426	0.81[CHD][hapmap];0.93[JPT][hapmap]
rs1597428	0.93[JPT][hapmap]
rs1597430	0.84[CHD][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap]
rs16914250	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs16914346	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs16914376	0.93[ASN][1000 genomes]
rs16914459	0.91[ASN][1000 genomes]
rs17758599	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]
rs1901055	0.93[JPT][hapmap]
rs1903311	0.90[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs1906070	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs203612	0.94[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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs203616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs203621	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203623	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs203624	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs203626	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs203629	0.80[EUR][1000 genomes]
rs203632	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203908	0.88[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs203925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs203928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs203930	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs203932	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs203933	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs203935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203936	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs203937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203939	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs203942	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs203945	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs203947	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs203949	0.95[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs203951	0.97[EUR][1000 genomes]
rs203960	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2084590	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2084591	0.86[ASN][1000 genomes]
rs2385812	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs34047312	0.90[ASN][1000 genomes]
rs34641787	0.90[ASN][1000 genomes]
rs34722367	0.93[ASN][1000 genomes]
rs34997857	0.91[ASN][1000 genomes]
rs35989044	0.93[ASN][1000 genomes]
rs36006902	0.93[ASN][1000 genomes]
rs420489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4330704	0.92[JPT][hapmap]
rs4398931	0.93[JPT][hapmap]
rs4448283	0.80[ASN][1000 genomes]
rs4448284	0.81[CHD][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap]
rs4543555	0.93[JPT][hapmap]
rs4577969	0.86[JPT][hapmap]
rs4633068	0.93[JPT][hapmap]
rs4873126	0.91[ASN][1000 genomes]
rs4873127	0.91[ASN][1000 genomes]
rs4873128	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[ASN][1000 genomes]
rs4873129	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs4873131	0.86[ASN][1000 genomes]
rs4873132	0.90[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4873133	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4873134	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4873135	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs4873137	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4873141	0.82[MEX][hapmap]
rs4873405	0.80[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs4873406	0.90[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs4873407	0.90[ASN][1000 genomes]
rs4873408	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[ASN][1000 genomes]
rs4873411	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4873412	0.92[ASN][1000 genomes]
rs4873413	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4873414	0.93[ASN][1000 genomes]
rs4873415	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4873416	0.93[ASN][1000 genomes]
rs4873417	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4873418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4873419	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4873420	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4873421	0.93[ASN][1000 genomes]
rs4873426	0.86[ASN][1000 genomes]
rs4873427	0.86[ASN][1000 genomes]
rs4873428	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs4873431	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs4873433	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs4873439	0.82[MEX][hapmap]
rs4873442	0.93[JPT][hapmap]
rs55889053	0.82[ASN][1000 genomes]
rs56007637	0.91[ASN][1000 genomes]
rs56725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62515375	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62516672	0.92[ASN][1000 genomes]
rs62516685	0.93[ASN][1000 genomes]
rs62516687	0.93[ASN][1000 genomes]
rs6472947	0.90[ASN][1000 genomes]
rs6981805	0.93[JPT][hapmap]
rs6983498	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs6986896	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6988843	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[ASN][1000 genomes]
rs6991753	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6996646	0.90[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs6999627	0.93[JPT][hapmap]
rs6999722	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs6999870	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7001686	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7002235	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[ASN][1000 genomes]
rs7004088	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7010037	0.93[ASN][1000 genomes]
rs7013247	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs7013995	0.90[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs7016161	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs7017642	0.93[JPT][hapmap]
rs7018082	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs721441	0.90[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs7386487	0.91[ASN][1000 genomes]
rs7464491	0.93[JPT][hapmap]
rs7817040	0.86[ASN][1000 genomes]
rs7817638	0.86[ASN][1000 genomes]
rs7820951	0.91[ASN][1000 genomes]
rs7821189	0.93[JPT][hapmap]
rs7824938	0.91[ASN][1000 genomes]
rs7825053	0.91[ASN][1000 genomes]
rs7825063	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7835849	0.86[ASN][1000 genomes]
rs870754	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs884561	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs898520	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[ASN][1000 genomes]
rs9298278	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs9298279	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs987356	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	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
5	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
6	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
7	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
rs203940	EFCAB1	cis	parietal	SCAN
rs203940	SNTG1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:50979200-50983400	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr8:50979600-50982600	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr8:50979800-50982600	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr8:50980200-50983400	Enhancers	Brain Germinal Matrix	brain
5	chr8:50980400-50982600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr8:50981800-50986800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr8:50982200-50982600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr8:50982200-50982600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:50982200-50982600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr8:50982400-50982600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:50982400-50982600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr8:50982400-50982600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr8:50982400-50982600	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr8:50982400-50982600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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