Variant report

Variant	rs11047880
Chromosome Location	chr12:25339843-25339844
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:25339080..25340582-chr12:25340786..25343717,2	MCF-7	breast:
2	chr12:25339039..25341718-chr12:25343903..25345457,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10842507	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10842508	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs10842509	0.90[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10842511	0.80[ASN][1000 genomes]
rs11047826	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs11047877	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11047882	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs11047892	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11047893	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11047911	0.80[EUR][1000 genomes]
rs11047918	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11533487	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs12228277	0.92[CEU][hapmap];0.90[CHB][hapmap];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12229161	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs12229450	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs12230737	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12230955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12423011	0.81[AMR][1000 genomes]
rs12423489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12423778	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs12424283	0.82[CHB][hapmap]
rs12427119	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs12427141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17328054	0.88[CEU][hapmap]
rs17329424	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs17387444	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs2970532	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[EUR][1000 genomes]
rs3782188	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs3924649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4356326	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4441109	1.00[JPT][hapmap]
rs4623993	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs4963852	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs4963853	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs4963857	0.91[CEU][hapmap];1.00[AFR][1000 genomes]
rs61016093	0.90[AMR][1000 genomes]
rs61761101	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61763584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73071272	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73073207	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7312175	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes]
rs7969931	0.82[CHB][hapmap]
rs7973746	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs7979296	1.00[CHB][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv515612	chr12:25272027-25341177	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv557797	chr12:25272027-25341177	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25339400-25340000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr12:25339400-25340200	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr12:25339400-25340200	Enhancers	Small Intestine	intestine
4	chr12:25339400-25340200	Flanking Active TSS	GM12878-XiMat	blood
5	chr12:25339400-25340200	Enhancers	HepG2	liver
6	chr12:25339400-25340400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr12:25339400-25340400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:25339400-25340400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr12:25339400-25340400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr12:25339600-25340000	Enhancers	Primary B cells from peripheral blood	blood
11	chr12:25339600-25340000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr12:25339600-25340000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
13	chr12:25339600-25340000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr12:25339600-25340000	Active TSS	Duodenum Mucosa	Duodenum
15	chr12:25339600-25340200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:25339600-25340200	Active TSS	Liver	Liver
17	chr12:25339600-25340200	Enhancers	Thymus	Thymus
18	chr12:25339600-25340400	Active TSS	Primary T cells fromperipheralblood	blood
19	chr12:25339600-25340400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr12:25339600-25340400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr12:25339600-25341000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:25339800-25340000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:25339800-25340200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr12:25339800-25340200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr12:25339800-25340200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:25339800-25340200	Flanking Active TSS	HMEC	breast
27	chr12:25339800-25340200	Flanking Active TSS	NHEK	skin
28	chr12:25339800-25343000	Enhancers	Osteobl	bone
29	chr12:25339800-25343200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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