Variant report

Variant	rs12423489
Chromosome Location	chr12:25342042-25342043
allele	C/T
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:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10842507	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs10842508	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10842509	0.92[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10842511	0.83[ASN][1000 genomes]
rs11047826	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs11047877	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11047880	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]
rs11047882	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11047892	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11047893	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11047911	0.81[EUR][1000 genomes]
rs11047918	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11533487	0.92[CEU][hapmap]
rs12228277	0.92[CEU][hapmap];0.92[CHB][hapmap];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12229161	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs12229450	0.92[CEU][hapmap]
rs12230737	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12230955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12423011	0.81[AMR][1000 genomes]
rs12423778	0.92[CEU][hapmap]
rs12424283	0.85[CHB][hapmap]
rs12427119	0.92[CEU][hapmap]
rs12427141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17329424	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs17387444	0.92[CEU][hapmap]
rs2970532	0.92[CEU][hapmap];0.92[CHB][hapmap];0.82[EUR][1000 genomes]
rs3782188	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs3924649	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs4356326	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4623993	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs4963852	0.92[CEU][hapmap]
rs4963853	0.92[CEU][hapmap]
rs4963857	0.84[CEU][hapmap];1.00[AFR][1000 genomes]
rs61016093	0.90[AMR][1000 genomes]
rs61761101	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61763584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73071272	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073207	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7309862	0.80[EUR][1000 genomes]
rs7312175	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes]
rs7969931	0.85[CHB][hapmap]
rs7973746	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs7979296	1.00[CHB][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25339800-25343000	Enhancers	Osteobl	bone
2	chr12:25339800-25343200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:25340000-25342800	Enhancers	NH-A	brain
4	chr12:25340000-25342800	Enhancers	NHDF-Ad	bronchial
5	chr12:25340000-25343000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr12:25340000-25343000	Enhancers	NHLF	lung
7	chr12:25340200-25347400	Weak transcription	Liver	Liver
8	chr12:25340600-25342600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:25340600-25342800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:25341000-25342400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:25341000-25347200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:25341000-25347200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr12:25341000-25347400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr12:25341000-25347400	Weak transcription	HMEC	breast
15	chr12:25341200-25346800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:25341200-25347400	Weak transcription	NHEK	skin
17	chr12:25341400-25347600	Weak transcription	HSMMtube	muscle
18	chr12:25341600-25342200	Enhancers	Hela-S3	cervix
19	chr12:25341800-25342400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:25341800-25342400	Enhancers	Rectal Smooth Muscle	rectum
21	chr12:25341800-25347400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:25342000-25347200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:25342000-25347400	Weak transcription	A549	lung

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