Variant report

Variant	rs12228617
Chromosome Location	chr12:39997867-39997868
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10877173	0.90[JPT][hapmap]
rs10877201	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172144	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs11172162	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs11172687	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs11172713	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172722	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11172794	0.90[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172848	0.90[JPT][hapmap]
rs11172896	0.81[ASN][1000 genomes]
rs11172897	0.82[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs12227286	0.90[JPT][hapmap]
rs12227668	0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12228013	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs12231004	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127129	0.90[JPT][hapmap]
rs17127138	0.89[JPT][hapmap]
rs4072006	0.86[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs4294600	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs59528535	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6581228	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133376	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7134015	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7307784	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7309234	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs7310178	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7312611	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73268358	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73268359	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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
15	nsv899019	chr12:39955802-40004906	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv519635	chr12:39985206-39998144	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv899020	chr12:39985206-40040331	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv899021	chr12:39989172-40053423	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39948800-40000000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:39963800-40010200	Weak transcription	Left Ventricle	heart
3	chr12:39966800-40009400	Weak transcription	Primary T cells from cord blood	blood
4	chr12:39980200-40006000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:39980200-40009200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:39981600-39999400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr12:39987800-40002000	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr12:39988000-39999600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:39992200-40000600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:39993800-40003400	Weak transcription	Adipose Nuclei	Adipose
11	chr12:39993800-40005600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr12:39994200-40002800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:39995200-39998200	Weak transcription	Brain Germinal Matrix	brain
14	chr12:39996000-39999400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:39996400-39998600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:39996400-39999800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:39996400-40007800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr12:39996800-40009400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:39997000-39998200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:39997400-39998200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr12:39997400-39998200	Strong transcription	GM12878-XiMat	blood
22	chr12:39997600-39999200	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:39997600-39999600	Enhancers	NHEK	skin
24	chr12:39997800-39999800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:39997800-40005800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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