Variant report

Variant	rs203930
Chromosome Location	chr8:50988837-50988838
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 149 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs10092399	0.81[MEX][hapmap]
rs10093604	0.91[CHB][hapmap]
rs10094935	0.81[JPT][hapmap]
rs10095985	0.84[CHB][hapmap];1.00[YRI][hapmap]
rs10098057	0.91[CHB][hapmap];0.95[MEX][hapmap]
rs10435582	0.83[ASN][1000 genomes]
rs10504098	0.82[CHB][hapmap];0.91[MEX][hapmap]
rs10504099	0.82[JPT][hapmap]
rs10808817	0.82[JPT][hapmap]
rs10957737	0.83[ASN][1000 genomes]
rs10957742	0.85[ASN][1000 genomes]
rs10957813	0.82[CHB][hapmap]
rs10957814	0.82[CHB][hapmap];0.95[MEX][hapmap]
rs10957828	0.91[CHB][hapmap]
rs11778998	0.82[CHB][hapmap]
rs11986160	0.82[CHB][hapmap];0.91[MEX][hapmap]
rs11991940	0.82[CHB][hapmap]
rs12056425	0.82[JPT][hapmap]
rs12056426	0.81[JPT][hapmap]
rs12541599	0.85[ASN][1000 genomes]
rs12542067	0.91[CHB][hapmap];0.95[MEX][hapmap]
rs12543077	0.91[MEX][hapmap]
rs12544631	0.82[JPT][hapmap]
rs12545915	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs12680748	0.82[JPT][hapmap]
rs13249415	0.81[JPT][hapmap]
rs13251587	0.81[JPT][hapmap]
rs13252320	0.85[JPT][hapmap]
rs13255224	0.85[ASN][1000 genomes]
rs13260265	0.82[CHB][hapmap];0.91[MEX][hapmap]
rs13266009	0.93[MKK][hapmap]
rs13282956	0.81[JPT][hapmap]
rs13340639	0.90[CHB][hapmap]
rs1349317	0.82[JPT][hapmap]
rs1375948	0.82[JPT][hapmap]
rs1380789	0.82[JPT][hapmap]
rs1380791	0.81[JPT][hapmap]
rs1380792	0.82[JPT][hapmap]
rs1450127	0.91[CHB][hapmap]
rs1484806	0.81[JPT][hapmap];0.93[MKK][hapmap];0.85[ASN][1000 genomes]
rs1486256	0.81[JPT][hapmap]
rs1486471	0.88[ASW][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap]
rs149992	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs149994	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1552316	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs1597426	0.82[JPT][hapmap]
rs1597428	0.82[JPT][hapmap]
rs1597430	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs1601298	0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs16914346	0.82[CHB][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap]
rs17758599	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]
rs1824462	0.82[JPT][hapmap]
rs1901055	0.82[JPT][hapmap]
rs1973259	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs203612	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs203616	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs203621	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs203623	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs203624	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs203626	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs203627	0.80[AMR][1000 genomes]
rs203629	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs203632	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs203908	0.96[CEU][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs203925	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs203928	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs203932	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs203933	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs203935	0.95[CEU][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs203936	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs203937	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs203938	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs203939	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs203940	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]
rs203942	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];0.99[ASN][1000 genomes]
rs203945	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs203947	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs203949	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs203951	0.96[EUR][1000 genomes]
rs203960	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2054743	0.81[JPT][hapmap]
rs2084590	0.91[CHB][hapmap]
rs2385699	0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2385812	0.91[CHB][hapmap];0.87[MEX][hapmap]
rs420489	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4398931	0.82[JPT][hapmap]
rs4448284	0.82[JPT][hapmap];0.82[MEX][hapmap]
rs4543555	0.82[JPT][hapmap]
rs4633068	0.82[JPT][hapmap]
rs4873128	0.82[CHB][hapmap];0.95[MEX][hapmap]
rs4873129	0.82[CHB][hapmap];0.91[MEX][hapmap]
rs4873132	0.91[CHB][hapmap]
rs4873133	0.91[CHB][hapmap]
rs4873134	0.91[CHB][hapmap]
rs4873135	0.91[CHB][hapmap];0.87[MEX][hapmap]
rs4873137	0.91[CHB][hapmap]
rs4873141	0.82[MEX][hapmap]
rs4873405	0.82[CHB][hapmap]
rs4873408	0.91[CHB][hapmap];0.95[MEX][hapmap]
rs4873411	0.91[CHB][hapmap]
rs4873413	0.82[CHB][hapmap]
rs4873415	0.82[CHB][hapmap]
rs4873417	0.91[CHB][hapmap]
rs4873418	0.82[CHB][hapmap]
rs4873419	0.82[CHB][hapmap]
rs4873420	0.82[CHB][hapmap]
rs4873428	0.91[CHB][hapmap];0.87[MEX][hapmap]
rs4873431	0.91[CHB][hapmap];0.87[MEX][hapmap]
rs4873433	0.91[CHB][hapmap];0.87[MEX][hapmap]
rs4873439	0.82[MEX][hapmap]
rs4873442	0.82[JPT][hapmap]
rs4873447	0.82[JPT][hapmap]
rs56725	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62515375	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6981805	0.82[JPT][hapmap]
rs6983498	0.91[CHB][hapmap];0.87[MEX][hapmap]
rs6986896	0.91[CHB][hapmap]
rs6988843	0.91[CHB][hapmap];0.91[MEX][hapmap]
rs6991753	0.91[CHB][hapmap]
rs6999627	0.82[JPT][hapmap]
rs6999722	0.91[CHB][hapmap]
rs6999870	0.91[CHB][hapmap]
rs7001686	0.91[CHB][hapmap]
rs7002235	0.82[CHB][hapmap];0.95[MEX][hapmap]
rs7004088	0.91[CHB][hapmap]
rs7013247	0.90[CHB][hapmap]
rs7016161	0.82[CHB][hapmap];0.91[MEX][hapmap]
rs7017642	0.82[JPT][hapmap]
rs7018082	0.91[CHB][hapmap]
rs7464491	0.81[JPT][hapmap]
rs7821189	0.82[JPT][hapmap]
rs7825063	0.91[CHB][hapmap]
rs870754	0.82[CHB][hapmap];0.82[MEX][hapmap]
rs884561	0.82[CHB][hapmap]
rs898520	0.82[CHB][hapmap];0.95[MEX][hapmap]
rs9298278	0.91[CHB][hapmap];0.95[MEX][hapmap]
rs9298279	0.91[CHB][hapmap];0.95[MEX][hapmap]
rs9643689	0.93[MKK][hapmap]
rs968944	0.82[JPT][hapmap]
rs968945	0.81[JPT][hapmap]
rs968947	0.82[JPT][hapmap]
rs987356	0.82[CHB][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
rs203930	SNTG1	cis	cerebellum	SCAN
rs203930	EFCAB1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:50987600-50991000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr8:50988200-50989000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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