Variant report

Variant	rs11172896
Chromosome Location	chr12:40017154-40017155
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40015362..40017426-chr12:40020461..40022505,2	MCF-7	breast:
2	chr12:40014171..40017168-chr12:40017549..40021409,3	K562	blood:

Variant related genes	Relation type
ENSG00000180116	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10877173	0.91[ASN][1000 genomes]
rs10877201	0.82[ASN][1000 genomes]
rs11172144	0.81[EUR][1000 genomes]
rs11172162	0.81[EUR][1000 genomes]
rs11172366	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172616	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172645	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172646	0.85[ASN][1000 genomes]
rs11172647	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172687	0.92[ASN][1000 genomes]
rs11172692	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172697	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11172722	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11172794	0.97[ASN][1000 genomes]
rs11172848	0.91[ASN][1000 genomes]
rs11172897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12227286	0.85[ASN][1000 genomes]
rs12227668	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12228013	0.81[EUR][1000 genomes]
rs12228617	0.81[ASN][1000 genomes]
rs12229160	0.83[EUR][1000 genomes]
rs12229370	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12230055	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12231004	0.81[ASN][1000 genomes]
rs17127129	0.81[EUR][1000 genomes]
rs35790935	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35858791	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4072006	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4285917	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4294600	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4298947	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4639970	0.83[EUR][1000 genomes]
rs57847223	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58036566	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59518553	0.85[ASN][1000 genomes]
rs59528535	0.97[ASN][1000 genomes]
rs61258856	0.81[EUR][1000 genomes]
rs6581228	0.81[ASN][1000 genomes]
rs7133599	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7134015	0.81[ASN][1000 genomes]
rs7294474	0.81[EUR][1000 genomes]
rs7302302	0.81[EUR][1000 genomes]
rs7307784	0.81[ASN][1000 genomes]
rs73088816	0.81[EUR][1000 genomes]
rs7309234	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73094447	0.81[EUR][1000 genomes]
rs73094449	0.81[EUR][1000 genomes]
rs73094488	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7310178	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310871	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73268358	0.97[ASN][1000 genomes]
rs73268359	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74086536	0.81[EUR][1000 genomes]
rs7970944	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40014200-40018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:40014800-40017800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:40015200-40017400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:40015200-40019800	Weak transcription	Brain Germinal Matrix	brain
5	chr12:40015200-40020200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:40015400-40017400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr12:40015400-40018000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:40015400-40018800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:40015400-40018800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr12:40015400-40019200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr12:40015600-40019000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr12:40016200-40018200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr12:40016600-40019000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr12:40016600-40019200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:40016600-40019600	Weak transcription	K562	blood
16	chr12:40016800-40017800	Weak transcription	Primary T cells from cord blood	blood
17	chr12:40016800-40017800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:40016800-40018800	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr12:40016800-40019000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr12:40017000-40017800	Weak transcription	GM12878-XiMat	blood
21	chr12:40017000-40021600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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