Variant report

Variant	rs7487999
Chromosome Location	chr12:40063237-40063238
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10047563	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10219652	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10444570	0.90[JPT][hapmap]
rs10735885	0.88[JPT][hapmap]
rs10747825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10747853	0.89[ASN][1000 genomes]
rs10747878	0.86[JPT][hapmap]
rs10783969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs10783993	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783994	0.94[ASN][1000 genomes]
rs10783998	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10784001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10784016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10784019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10784051	0.89[JPT][hapmap]
rs10784059	0.90[JPT][hapmap]
rs10877305	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877335	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877337	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877369	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10877383	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10877410	0.81[AMR][1000 genomes]
rs11173013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11173257	0.85[ASN][1000 genomes]
rs11173260	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11173262	0.83[ASN][1000 genomes]
rs11173376	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11173440	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs11173446	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs11173459	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs11173494	0.91[CEU][hapmap];0.89[JPT][hapmap]
rs11173507	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs11173541	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs11173550	0.90[JPT][hapmap]
rs12229203	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs12229301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12229418	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs12230687	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs12823801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12825223	0.83[ASN][1000 genomes]
rs4077987	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4129365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4238072	0.90[JPT][hapmap]
rs4238073	0.90[JPT][hapmap]
rs4312128	0.90[JPT][hapmap]
rs4337105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4357762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4405390	0.89[JPT][hapmap]
rs4411336	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4417381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4417382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4495951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4594067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4767949	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4768166	0.92[CEU][hapmap]
rs4768168	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4768169	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4768170	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57244766	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs58418587	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61933102	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61933154	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6421191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6421195	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6421196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6421197	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6421198	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6581250	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6581263	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6581265	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6581266	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6581270	0.92[CEU][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6581271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6581272	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6581294	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7136929	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7296585	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7485345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7486196	0.95[ASN][1000 genomes]
rs7486621	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7486631	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs7952735	0.94[ASN][1000 genomes]
rs7956577	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7959285	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7959905	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7961070	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7961346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7973312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7980636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs9325166	0.92[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1037457	chr12:39898349-40245401	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv541480	chr12:39898349-40245401	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv899014	chr12:39946354-40068896	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv899015	chr12:39946354-40118249	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv899017	chr12:39949147-40081619	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv899018	chr12:39949147-40111761	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv899022	chr12:40014427-40111761	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
9	nsv899023	chr12:40046408-40111761	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
10	nsv899024	chr12:40046408-40188870	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40062600-40064000	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr12:40062600-40064200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr12:40062600-40064400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:40062800-40063800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr12:40062800-40064400	Enhancers	Primary T cells fromperipheralblood	blood
6	chr12:40063000-40064200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:40063000-40064400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:40063000-40064400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr12:40063000-40064600	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr12:40063200-40063600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr12:40063200-40064000	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr12:40063200-40064000	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr12:40063200-40064200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:40063200-40064400	Enhancers	Primary T helper cells fromperipheralblood	blood

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