Variant report

Variant	rs12218216
Chromosome Location	chr10:96342020-96342021
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1018602	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1042192	0.81[LWK][hapmap]
rs1042194	0.81[LWK][hapmap]
rs10786168	0.87[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs10786169	0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs10786170	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10882460	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs10882463	0.87[MEX][hapmap];0.83[TSI][hapmap]
rs10882470	0.84[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs10882474	0.87[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs10882477	0.84[EUR][1000 genomes]
rs10882481	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11187948	0.84[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs11187952	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs11187958	0.80[EUR][1000 genomes]
rs11187966	0.81[EUR][1000 genomes]
rs11187972	0.86[CEU][hapmap]
rs11187980	0.81[MEX][hapmap];0.81[TSI][hapmap]
rs11187998	0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap]
rs11188005	0.81[EUR][1000 genomes]
rs11188009	0.86[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs11188012	0.80[JPT][hapmap]
rs11188015	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11188016	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11188017	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11188019	0.80[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs11188026	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11188030	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11188038	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11188039	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11188040	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];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11188041	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11638	0.80[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs12218213	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12219906	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12220588	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];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12221475	0.84[CEU][hapmap]
rs12570013	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12573638	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1326838	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1326839	0.86[EUR][1000 genomes]
rs1359262	0.81[EUR][1000 genomes]
rs1359263	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1749356	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1854034	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1854035	0.86[EUR][1000 genomes]
rs1889486	0.84[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs1926712	0.84[LWK][hapmap]
rs1931757	0.80[JPT][hapmap]
rs1969815	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1977290	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1977291	0.80[JPT][hapmap]
rs1980741	0.80[JPT][hapmap]
rs2012670	0.87[EUR][1000 genomes]
rs2148553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274096	0.83[EUR][1000 genomes]
rs2274417	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];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2281791	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs2281890	0.81[LWK][hapmap]
rs2860760	0.81[EUR][1000 genomes]
rs2860821	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];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2860838	0.81[LWK][hapmap]
rs34814196	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35774063	0.84[EUR][1000 genomes]
rs3740358	0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs3758522	0.84[EUR][1000 genomes]
rs3758523	0.85[EUR][1000 genomes]
rs3781262	0.87[EUR][1000 genomes]
rs4316436	0.84[EUR][1000 genomes]
rs4351744	0.80[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs4421688	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4611135	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4918401	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4918402	0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs4918403	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4918404	0.83[EUR][1000 genomes]
rs4918409	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4918411	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4918412	0.84[EUR][1000 genomes]
rs4918417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4918418	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4918419	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs493088	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs56020662	0.81[EUR][1000 genomes]
rs6583944	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6583945	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6583946	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6583954	0.84[LWK][hapmap]
rs68046102	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs692872	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs701885	0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs7068337	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7078478	0.80[JPT][hapmap]
rs7078811	0.80[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs7079934	0.84[EUR][1000 genomes]
rs7083898	0.80[JPT][hapmap]
rs7086462	0.84[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs7087472	0.82[EUR][1000 genomes]
rs717238	0.84[LWK][hapmap]
rs7393251	0.85[CEU][hapmap]
rs7900135	0.81[LWK][hapmap]
rs7906843	0.83[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs7906968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7913343	0.83[CEU][hapmap]
rs7921721	0.80[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs912466	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs932809	0.84[LWK][hapmap]
rs955694	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]

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	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1053747	chr10:96211618-96366396	Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12218216	KIF11	cis	cerebellum	SCAN
rs12218216	HELLS	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96306400-96357200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr10:96306400-96365600	Weak transcription	Esophagus	oesophagus
3	chr10:96306400-96370400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr10:96306400-96370600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr10:96306400-96371000	Weak transcription	Ovary	ovary
6	chr10:96306600-96349800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr10:96306600-96353800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr10:96306600-96379200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:96306800-96348000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr10:96306800-96348200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr10:96306800-96348400	Weak transcription	Primary B cells from cord blood	blood
12	chr10:96306800-96349800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr10:96306800-96357200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr10:96306800-96373000	Weak transcription	Primary T cells from cord blood	blood
15	chr10:96307000-96358200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr10:96307000-96375000	Weak transcription	Osteobl	bone
17	chr10:96307200-96371200	Weak transcription	Fetal Brain Male	brain
18	chr10:96307600-96356000	Weak transcription	NHDF-Ad	bronchial
19	chr10:96307600-96373200	Weak transcription	Brain Germinal Matrix	brain
20	chr10:96307800-96348200	Weak transcription	NHEK	skin
21	chr10:96307800-96373000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr10:96308000-96373200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr10:96309400-96354000	Weak transcription	K562	blood
24	chr10:96309600-96372800	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr10:96309600-96377000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr10:96312200-96354000	Weak transcription	Gastric	stomach
27	chr10:96312800-96372200	Strong transcription	Dnd41	blood
28	chr10:96314200-96373400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr10:96315000-96369200	Weak transcription	Fetal Kidney	kidney
30	chr10:96315600-96343800	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr10:96315600-96345200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr10:96316000-96371400	Weak transcription	Fetal Brain Female	brain
33	chr10:96316000-96374000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr10:96316200-96357600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr10:96316200-96373000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr10:96317000-96372600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr10:96317400-96348000	Weak transcription	NH-A	brain
38	chr10:96321000-96353200	Weak transcription	Fetal Intestine Large	intestine
39	chr10:96324000-96356600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr10:96324000-96376600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr10:96324200-96353800	Weak transcription	Primary B cells from peripheral blood	blood
42	chr10:96324200-96365600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr10:96325800-96348200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr10:96325800-96376000	Weak transcription	NHLF	lung
45	chr10:96327000-96347400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr10:96327800-96348000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr10:96330200-96348000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr10:96330600-96347800	Weak transcription	HUVEC	blood vessel
49	chr10:96331000-96377400	Weak transcription	Placenta	Placenta
50	chr10:96331200-96361800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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