Variant report

Variant	rs897388
Chromosome Location	chr12:123318392-123318393
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123317720..123322313-chr12:123372173..123377754,7	MCF-7	breast:
2	chr12:123317692..123320507-chr12:123463597..123466562,3	MCF-7	breast:
3	chr12:123257747..123262116-chr12:123318149..123321331,4	MCF-7	breast:
4	chr12:123237061..123238610-chr12:123318389..123320839,2	MCF-7	breast:
5	chr12:123318351..123322726-chr12:123344658..123350717,8	MCF-7	breast:
6	chr12:123303995..123306395-chr12:123315559..123318480,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139722	Chromatin interaction
ENSG00000130783	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000256152	Chromatin interaction
ENSG00000182196	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000139726	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1026395	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1037593	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10744394	0.88[EUR][1000 genomes]
rs10744439	0.88[EUR][1000 genomes]
rs10773599	1.00[JPT][hapmap]
rs10847742	1.00[JPT][hapmap]
rs10847749	1.00[JPT][hapmap]
rs10847751	1.00[JPT][hapmap]
rs10847775	1.00[JPT][hapmap]
rs10847910	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs10848148	1.00[JPT][hapmap]
rs11059729	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs11060152	1.00[JPT][hapmap]
rs11060211	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11060932	1.00[JPT][hapmap]
rs11060999	1.00[JPT][hapmap]
rs12311043	1.00[JPT][hapmap]
rs1260121	1.00[JPT][hapmap]
rs1671684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1671686	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1671687	1.00[JPT][hapmap]
rs1696327	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1798563	1.00[JPT][hapmap]
rs1975761	1.00[JPT][hapmap]
rs2061099	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2271048	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2343107	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2604851	0.81[EUR][1000 genomes]
rs2649895	1.00[JPT][hapmap]
rs2649896	1.00[JPT][hapmap]
rs2649903	1.00[JPT][hapmap]
rs2649904	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656812	1.00[JPT][hapmap]
rs2656815	0.82[EUR][1000 genomes]
rs3844369	1.00[JPT][hapmap]
rs4307760	1.00[JPT][hapmap]
rs4759351	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4759352	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4759353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4759354	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4759384	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4759388	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4759438	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs651683	1.00[JPT][hapmap]
rs7138257	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7298176	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7303973	0.81[EUR][1000 genomes]
rs7306047	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs7306948	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs7485652	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7487095	1.00[ASN][1000 genomes]
rs7957643	1.00[JPT][hapmap]
rs7958155	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs839352	0.83[AMR][1000 genomes]
rs839354	1.00[JPT][hapmap]
rs839357	0.83[AMR][1000 genomes]
rs897384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs937765	0.92[EUR][1000 genomes]
rs967281	1.00[JPT][hapmap]
rs9795629	1.00[JPT][hapmap]

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	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv899574	chr12:123316566-123360151	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123305800-123318800	Weak transcription	Pancreas	Pancrea
2	chr12:123310400-123319200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:123311000-123318800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:123311200-123319000	Weak transcription	Aorta	Aorta
5	chr12:123311400-123318800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr12:123311600-123318800	Weak transcription	NHDF-Ad	bronchial
7	chr12:123312200-123318800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:123312400-123318800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:123312400-123318800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:123312400-123318800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:123312400-123318800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:123312400-123318800	Weak transcription	Brain Substantia Nigra	brain
13	chr12:123312600-123318800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:123313800-123319200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:123315600-123319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:123315800-123318800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:123315800-123318800	Weak transcription	A549	lung
18	chr12:123315800-123318800	Weak transcription	K562	blood
19	chr12:123315800-123318800	Weak transcription	NHLF	lung
20	chr12:123316000-123318800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:123316000-123318800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:123316000-123318800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:123316000-123318800	Weak transcription	Placenta	Placenta
24	chr12:123316000-123318800	Weak transcription	NHEK	skin
25	chr12:123316200-123318800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:123316200-123318800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:123316200-123318800	Weak transcription	HMEC	breast
28	chr12:123316400-123319200	Weak transcription	Gastric	stomach
29	chr12:123317800-123318800	Enhancers	Fetal Brain Male	brain
30	chr12:123318200-123318400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
31	chr12:123318200-123318400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
32	chr12:123318200-123318600	Weak transcription	Stomach Mucosa	stomach
33	chr12:123318200-123318600	Weak transcription	Hela-S3	cervix
34	chr12:123318200-123318800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:123318200-123318800	Enhancers	Fetal Brain Female	brain

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