Variant report

Variant	rs17686196
Chromosome Location	chr8:50958890-50958891
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1000638	1.00[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs1000639	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10096871	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs10098057	0.95[CEU][hapmap]
rs10504094	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10504096	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10504098	0.95[CEU][hapmap]
rs10957764	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];0.92[MKK][hapmap];1.00[TSI][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]
rs10957802	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10957813	0.95[CEU][hapmap]
rs10957814	0.95[CEU][hapmap]
rs11778998	0.95[CEU][hapmap]
rs11781074	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];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11986160	0.95[CEU][hapmap]
rs11991940	0.95[CEU][hapmap]
rs12541488	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[YRI][hapmap]
rs12541543	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs12541852	1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[ASN][1000 genomes]
rs12542067	0.95[CEU][hapmap]
rs12544986	0.94[CEU][hapmap]
rs12545107	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];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][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]
rs12545263	0.88[EUR][1000 genomes]
rs12548940	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap]
rs13251700	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13255893	1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs13260265	0.95[CEU][hapmap]
rs13270234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13270712	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs13271983	0.98[EUR][1000 genomes]
rs13273543	0.82[ASN][1000 genomes]
rs13280089	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13340639	0.83[CEU][hapmap]
rs16914346	0.95[CEU][hapmap]
rs17685307	0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs1903311	1.00[CEU][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs2106156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2157736	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34047312	0.89[EUR][1000 genomes]
rs34641787	0.90[EUR][1000 genomes]
rs34908792	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35093761	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35122483	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35418717	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35609530	0.82[ASN][1000 genomes]
rs35989044	0.99[EUR][1000 genomes]
rs4873128	0.95[CEU][hapmap]
rs4873129	0.95[CEU][hapmap]
rs4873405	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4873406	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4873407	0.89[EUR][1000 genomes]
rs4873408	0.95[CEU][hapmap]
rs4873411	0.95[CEU][hapmap]
rs4873415	0.95[CEU][hapmap]
rs4873417	0.95[CEU][hapmap]
rs4873418	0.95[CEU][hapmap]
rs4873419	0.95[CEU][hapmap]
rs4873420	0.95[CEU][hapmap]
rs4873421	0.95[CEU][hapmap]
rs55743661	0.82[ASN][1000 genomes]
rs55760013	0.82[ASN][1000 genomes]
rs56413317	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62516686	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6472947	0.90[EUR][1000 genomes]
rs66541944	0.82[ASN][1000 genomes]
rs67043411	0.82[ASN][1000 genomes]
rs6986896	0.95[CEU][hapmap]
rs6988843	0.95[CEU][hapmap]
rs6996646	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs6999722	0.94[CEU][hapmap]
rs6999870	0.95[CEU][hapmap]
rs7001686	0.95[CEU][hapmap]
rs7002235	0.95[CEU][hapmap]
rs7004088	0.95[CEU][hapmap]
rs7013995	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7016161	0.95[CEU][hapmap]
rs721441	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7820951	0.94[EUR][1000 genomes]
rs7825063	0.95[CEU][hapmap]
rs870754	0.95[CEU][hapmap]
rs884561	0.95[CEU][hapmap]
rs898520	0.95[CEU][hapmap]
rs9298278	0.95[CEU][hapmap]
rs9298279	0.95[CEU][hapmap]
rs9650160	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs987356	0.95[CEU][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
rs17686196	SNTG1	cis	cerebellum	SCAN
rs17686196	EFCAB1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:50952800-50969800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:50958200-50959000	Enhancers	Hela-S3	cervix

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