Variant report

Variant	rs12763178
Chromosome Location	chr10:91565990-91565991
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10430645	1.00[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs10430646	1.00[CEU][hapmap]
rs1048057	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs10509579	1.00[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs1062465	1.00[CEU][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs10785896	0.94[CEU][hapmap]
rs10785907	0.80[EUR][1000 genomes]
rs10881614	0.94[CEU][hapmap];0.88[TSI][hapmap]
rs10881618	0.94[CEU][hapmap];0.85[TSI][hapmap]
rs10881619	0.94[CEU][hapmap]
rs10881628	1.00[CEU][hapmap]
rs10881629	1.00[CEU][hapmap]
rs10881631	1.00[CEU][hapmap]
rs10881632	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10881646	0.92[CEU][hapmap]
rs10881647	1.00[CEU][hapmap]
rs10881657	0.80[EUR][1000 genomes]
rs10881664	1.00[CEU][hapmap]
rs10881666	1.00[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs10881667	0.80[EUR][1000 genomes]
rs10881668	0.80[EUR][1000 genomes]
rs10881669	0.80[EUR][1000 genomes]
rs10881670	0.80[EUR][1000 genomes]
rs10982	0.80[EUR][1000 genomes]
rs11185825	0.94[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap]
rs11185861	1.00[CEU][hapmap]
rs11185867	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11185878	0.80[EUR][1000 genomes]
rs11185879	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11185880	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs11185881	0.80[EUR][1000 genomes]
rs11185884	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11185886	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11185889	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11185890	0.82[EUR][1000 genomes]
rs11185892	0.90[EUR][1000 genomes]
rs11813204	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11813214	0.80[EUR][1000 genomes]
rs11814174	0.85[YRI][hapmap]
rs11816741	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12243552	0.80[EUR][1000 genomes]
rs12250365	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs12253793	0.80[EUR][1000 genomes]
rs12254296	0.80[EUR][1000 genomes]
rs12264026	0.80[EUR][1000 genomes]
rs12767644	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12773740	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12773865	0.83[ASN][1000 genomes]
rs12776628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12779880	0.81[ASN][1000 genomes]
rs12948	0.80[EUR][1000 genomes]
rs1409358	0.94[CEU][hapmap];0.88[TSI][hapmap]
rs1555868	1.00[CEU][hapmap]
rs17125278	0.93[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1886997	1.00[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs2026550	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2077946	0.93[CEU][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs2182396	1.00[CEU][hapmap]
rs34089128	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35754486	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3740037	1.00[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs3758385	1.00[CEU][hapmap]
rs3824609	1.00[CEU][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs4126596	0.80[EUR][1000 genomes]
rs61872460	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6586218	1.00[CEU][hapmap]
rs7070916	0.83[ASN][1000 genomes]
rs7074093	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7076259	0.94[CEU][hapmap];0.88[TSI][hapmap]
rs7077349	1.00[CEU][hapmap]
rs7081362	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7085805	1.00[CEU][hapmap]
rs7087240	0.94[CEU][hapmap]
rs7087789	0.94[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs7088104	0.94[CEU][hapmap]
rs7089473	1.00[CEU][hapmap]
rs7092444	1.00[CEU][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs7095702	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7095818	1.00[CEU][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs7096466	1.00[CEU][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs7096826	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7097496	0.94[CEU][hapmap]
rs7100603	0.94[CEU][hapmap];0.88[TSI][hapmap]
rs716781	0.94[CEU][hapmap]
rs727427	0.94[CEU][hapmap]
rs735936	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7895379	1.00[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs7896461	0.80[EUR][1000 genomes]
rs7898670	1.00[CEU][hapmap]
rs7907852	0.94[CEU][hapmap];0.85[TSI][hapmap]
rs7909550	1.00[CEU][hapmap]
rs7912464	1.00[CEU][hapmap]
rs7914590	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7919866	0.80[EUR][1000 genomes]
rs7921817	0.80[EUR][1000 genomes]
rs8181361	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs8181406	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9325443	0.94[CEU][hapmap];0.88[TSI][hapmap]
rs9325444	0.94[CEU][hapmap]
rs962524	1.00[CEU][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs9663129	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046241	chr10:91478562-91614437	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv869080	chr10:91498641-91712834	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1036581	chr10:91526705-91691536	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12763178	KIF20B	cis	cerebellum	SCAN
rs12763178	RP11-248C1.3	cis	Artery Tibial	GTEx
rs12763178	IFIT1	cis	cerebellum	SCAN
rs12763178	LINC00865	cis	Artery Tibial	GTEx
rs12763178	KIF20B	cis	parietal	SCAN
rs12763178	LINC00865	cis	Nerve Tibial	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91565400-91566000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr10:91565600-91566000	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr10:91565800-91566600	Enhancers	GM12878-XiMat	blood

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