Variant report

Variant	rs6581187
Chromosome Location	chr12:39952412-39952413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10876972	0.83[EUR][1000 genomes]
rs10877100	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172108	0.84[EUR][1000 genomes]
rs11172120	0.83[EUR][1000 genomes]
rs11172174	0.83[EUR][1000 genomes]
rs11172293	0.88[EUR][1000 genomes]
rs11172319	0.82[ASN][1000 genomes]
rs11172357	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172386	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172392	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172492	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172493	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172526	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172541	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172625	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172638	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172650	0.89[ASN][1000 genomes]
rs11172661	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4284427	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4320988	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4378431	0.84[ASN][1000 genomes]
rs4390378	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4451772	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4466883	0.86[ASN][1000 genomes]
rs4475956	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4492858	0.89[EUR][1000 genomes]
rs4500523	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58240943	0.83[EUR][1000 genomes]
rs58613501	0.83[EUR][1000 genomes]
rs60263267	0.80[ASN][1000 genomes]
rs6581188	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73094410	0.83[EUR][1000 genomes]
rs73096532	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7316073	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7485730	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7962283	0.83[EUR][1000 genomes]
rs7965222	0.85[EUR][1000 genomes]
rs7968837	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv1039645	chr12:39903123-40022029	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats 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	5 gene(s)	inside rSNPs	diseases
5	nsv522940	chr12:39946354-39998144	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv469359	chr12:39946354-40034699	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv558591	chr12:39946354-40034699	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv469361	chr12:39946354-40042220	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv558592	chr12:39946354-40042220	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv899016	chr12:39949147-40004906	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
13	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
14	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

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39948800-40000000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:39949600-39953000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr12:39950200-39953000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
4	chr12:39950600-39952800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:39951000-39955400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:39951200-39953000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:39951200-39953000	ZNF genes & repeats	Adipose Nuclei	Adipose
8	chr12:39951400-39952600	ZNF genes & repeats	Spleen	Spleen
9	chr12:39951400-39953000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:39951400-39953200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:39951400-39953800	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr12:39951400-39953800	ZNF genes & repeats	GM12878-XiMat	blood
13	chr12:39951400-39955000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr12:39951600-39953400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
15	chr12:39951600-39953600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr12:39951600-39953800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:39951800-39952600	Weak transcription	Brain Angular Gyrus	brain
18	chr12:39951800-39952800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:39952000-39953800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
20	chr12:39952200-39953000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
21	chr12:39952200-39955000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
22	chr12:39952400-39953400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
23	chr12:39952400-39953600	ZNF genes & repeats	Primary T cells from cord blood	blood

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