Variant report

Variant	rs6421195
Chromosome Location	chr12:40080088-40080089
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10047563	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10219652	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10444570	0.89[AMR][1000 genomes]
rs10747825	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10747853	0.94[ASN][1000 genomes]
rs10747877	0.81[AMR][1000 genomes]
rs10747878	0.83[AMR][1000 genomes]
rs10783993	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783994	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783998	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784001	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784016	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10784034	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10784051	0.83[AMR][1000 genomes]
rs10784059	0.83[AMR][1000 genomes]
rs10877305	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877335	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877337	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877369	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877410	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172998	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11173257	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11173260	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11173262	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11173376	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11173394	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11173401	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11173423	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11173424	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11173428	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11173433	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11173434	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11173440	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11173446	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11173459	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11173494	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11173507	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11173541	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11173550	0.83[AMR][1000 genomes]
rs11173551	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11173553	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11532458	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12229203	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12229418	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12230687	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12823801	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12825223	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4077987	0.82[ASN][1000 genomes]
rs4238072	0.87[AMR][1000 genomes]
rs4238073	0.87[AMR][1000 genomes]
rs4255599	0.87[AMR][1000 genomes]
rs4255600	0.87[AMR][1000 genomes]
rs4312128	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4322461	0.87[AMR][1000 genomes]
rs4381428	0.89[AMR][1000 genomes]
rs4388963	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4405390	0.87[AMR][1000 genomes]
rs4405391	0.87[AMR][1000 genomes]
rs4411336	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4417381	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4417382	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4556618	0.85[AMR][1000 genomes]
rs4594067	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767949	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768168	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768169	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768170	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57244766	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58418587	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58755301	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61477638	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs61931185	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61931208	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61931211	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61933102	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933154	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61933157	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61933158	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6421196	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6421197	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6421198	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581265	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581266	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581270	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581271	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581272	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581294	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7136929	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301886	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7302849	0.87[AMR][1000 genomes]
rs7308955	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7485345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7486196	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7486621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7487999	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7952735	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7956577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959905	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7961070	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961346	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7964129	0.81[AMR][1000 genomes]
rs7969282	0.87[AMR][1000 genomes]
rs7973312	0.91[EUR][1000 genomes]
rs7980636	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
5	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
6	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
7	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
8	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
9	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:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40077600-40085000	Weak transcription	Primary T cells from cord blood	blood
2	chr12:40077800-40080400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:40078000-40081000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:40078800-40080400	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr12:40078800-40085200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:40079000-40080400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr12:40079000-40080400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:40079200-40080400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:40079200-40080400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:40079400-40080400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr12:40079400-40080600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr12:40079400-40080800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr12:40079600-40080200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr12:40079800-40080400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr12:40080000-40080400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr12:40080000-40080400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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