Variant report

Variant	rs12465422
Chromosome Location	chr2:152920126-152920127
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	chr2:152918845..152920622-chr2:152923227..152925166,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10930910	0.81[GIH][hapmap]
rs12465272	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12470410	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12472173	0.92[CHB][hapmap]
rs12992504	0.92[CHB][hapmap]
rs12995261	0.89[CEU][hapmap]
rs13009432	0.92[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13009895	0.81[EUR][1000 genomes]
rs13011110	0.91[CHB][hapmap]
rs13027217	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1401778	0.96[CEU][hapmap]
rs1519708	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1519713	0.92[CHB][hapmap]
rs17270332	0.92[CHB][hapmap]
rs17326005	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17326047	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17397935	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1879136	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2881188	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34139080	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35060770	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35343813	0.92[CHB][hapmap]
rs35529845	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35802014	0.83[ASN][1000 genomes]
rs35871736	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4494739	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4608509	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4664074	0.80[ASN][1000 genomes]
rs4664076	0.83[CHD][hapmap]
rs4664514	0.92[CHB][hapmap]
rs4664523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55700223	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55983612	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57702516	0.80[ASN][1000 genomes]
rs6433733	0.92[CHB][hapmap]
rs6433779	0.96[CEU][hapmap]
rs6719674	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6727569	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6727592	0.92[CHB][hapmap]
rs6734642	0.92[CHB][hapmap]
rs6736011	0.80[EUR][1000 genomes]
rs6736449	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs6745978	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751763	0.92[CHB][hapmap]
rs6756595	0.92[CHB][hapmap]
rs6758996	0.80[ASN][1000 genomes]
rs7349251	0.92[CHB][hapmap]
rs7558481	0.92[CHB][hapmap]
rs7564177	0.92[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap]
rs7571637	0.92[CHB][hapmap]
rs7582231	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7582644	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7585215	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7598593	0.92[CHB][hapmap]
rs7602165	0.92[CHB][hapmap]
rs952340	0.92[CHB][hapmap]

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	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv875290	chr2:152803129-152920126	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	esv1847028	chr2:152863856-153045036	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 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	chr2:152916000-152932000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:152918000-152920600	Enhancers	Fetal Brain Male	brain
3	chr2:152918800-152920200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:152918800-152920200	Enhancers	HSMM	muscle
5	chr2:152918800-152920400	Enhancers	Fetal Muscle Leg	muscle
6	chr2:152918800-152920400	Enhancers	NHLF	lung
7	chr2:152918800-152920800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:152919000-152920400	Enhancers	Fetal Thymus	thymus
9	chr2:152919000-152920600	Enhancers	Fetal Lung	lung
10	chr2:152919000-152920800	Enhancers	Fetal Brain Female	brain
11	chr2:152919200-152920600	Enhancers	A549	lung
12	chr2:152919400-152920200	Enhancers	Adipose Nuclei	Adipose
13	chr2:152919400-152920200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:152919400-152920600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:152919400-152920800	Enhancers	HSMMtube	muscle
16	chr2:152919400-152922600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:152919800-152920200	Weak transcription	Fetal Stomach	stomach
18	chr2:152919800-152920200	Bivalent Enhancer	Osteobl	bone
19	chr2:152919800-152920400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr2:152919800-152920600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:152920000-152920200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:152920000-152920400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:152920000-152920600	Bivalent Enhancer	NHDF-Ad	bronchial
24	chr2:152920000-152920800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:152920000-152920800	Enhancers	Stomach Smooth Muscle	stomach

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