Variant report

Variant	rs490008
Chromosome Location	chr6:128030957-128030958
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1080436	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1115440	1.00[ASN][1000 genomes]
rs11759373	1.00[CHD][hapmap]
rs12192864	0.88[AMR][1000 genomes]
rs12194062	1.00[CHD][hapmap]
rs12201026	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201136	1.00[CEU][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1318049	1.00[ASN][1000 genomes]
rs1374983	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1445644	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1448056	1.00[ASN][1000 genomes]
rs1512455	1.00[ASN][1000 genomes]
rs1512456	1.00[ASN][1000 genomes]
rs1512461	1.00[ASN][1000 genomes]
rs1512462	1.00[ASN][1000 genomes]
rs1512463	1.00[ASN][1000 genomes]
rs1533186	1.00[ASN][1000 genomes]
rs156062	1.00[CHD][hapmap]
rs1588647	1.00[ASN][1000 genomes]
rs1588648	1.00[ASN][1000 genomes]
rs1606331	1.00[ASN][1000 genomes]
rs1606333	1.00[ASN][1000 genomes]
rs172008	1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs1828612	1.00[ASN][1000 genomes]
rs1913079	1.00[ASN][1000 genomes]
rs1913080	1.00[ASN][1000 genomes]
rs1949173	1.00[CHD][hapmap]
rs1980060	1.00[ASN][1000 genomes]
rs2068626	1.00[ASN][1000 genomes]
rs2166835	1.00[ASN][1000 genomes]
rs2221878	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs269990	0.80[AMR][1000 genomes]
rs269996	1.00[YRI][hapmap]
rs269999	1.00[CHD][hapmap]
rs270002	1.00[CHD][hapmap]
rs270003	1.00[CHD][hapmap];0.87[MKK][hapmap]
rs270007	0.80[AMR][1000 genomes]
rs270008	0.80[AMR][1000 genomes]
rs270011	1.00[CHD][hapmap]
rs270013	1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs270014	1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs270015	1.00[ASW][hapmap];1.00[CHD][hapmap];0.94[MKK][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes]
rs2786230	0.81[EUR][1000 genomes]
rs3009961	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs34471518	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35158225	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3948102	1.00[ASN][1000 genomes]
rs486235	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897215	1.00[ASN][1000 genomes]
rs500192	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs505827	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525267	0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs550875	0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs553910	0.82[EUR][1000 genomes]
rs564461	0.89[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579177	1.00[CHD][hapmap];0.84[GIH][hapmap]
rs580388	0.81[EUR][1000 genomes]
rs583072	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583956	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs607496	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614885	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620250	0.85[TSI][hapmap]
rs648151	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651416	0.96[CEU][hapmap]
rs655681	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569495	1.00[ASN][1000 genomes]
rs6569497	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6569504	1.00[CHD][hapmap]
rs669663	0.96[CEU][hapmap];0.85[YRI][hapmap]
rs67116440	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs674751	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680544	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs682312	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683202	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909510	1.00[ASN][1000 genomes]
rs6920033	1.00[ASN][1000 genomes]
rs6921497	1.00[ASN][1000 genomes]
rs6921729	1.00[CHD][hapmap]
rs766819	1.00[ASN][1000 genomes]
rs766820	1.00[ASN][1000 genomes]
rs7746884	1.00[ASN][1000 genomes]
rs7747070	1.00[ASN][1000 genomes]
rs7749538	1.00[ASN][1000 genomes]
rs7749800	1.00[ASN][1000 genomes]
rs7751559	1.00[ASN][1000 genomes]
rs7751643	1.00[ASN][1000 genomes]
rs7761797	1.00[ASN][1000 genomes]
rs7766541	1.00[ASN][1000 genomes]
rs9385434	1.00[ASN][1000 genomes]
rs9398851	1.00[ASN][1000 genomes]
rs956693	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886638	chr6:127954614-128087172	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv886639	chr6:127954614-128109244	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv886640	chr6:127961263-128096587	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv886641	chr6:127971136-128085283	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv886642	chr6:127971136-128096587	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv886643	chr6:127971136-128109244	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv886644	chr6:127976408-128109244	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv886645	chr6:127977160-128085283	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv886646	chr6:127977160-128087172	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv886647	chr6:127977160-128109244	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv886648	chr6:127983009-128109244	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv819539	chr6:128030905-128031235	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	n/a

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128024400-128041200	Strong transcription	Primary T cells fromperipheralblood	blood
2	chr6:128024600-128051400	Strong transcription	Fetal Thymus	thymus
3	chr6:128024800-128041000	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr6:128024800-128042400	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr6:128025200-128047400	Strong transcription	Primary T cells from cord blood	blood
6	chr6:128026200-128031400	Weak transcription	Fetal Heart	heart
7	chr6:128026400-128049200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:128026600-128036600	Weak transcription	Dnd41	blood
9	chr6:128028200-128035600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:128028600-128031400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr6:128029000-128033800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:128029200-128031000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:128029200-128031000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:128029200-128031400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:128029400-128031400	Weak transcription	Thymus	Thymus
16	chr6:128030000-128034400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:128030800-128033200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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