Variant report

Variant	rs2100500
Chromosome Location	chr12:123318626-123318627
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	chr12:123318440..123320805-chr12:123633475..123636263,2	MCF-7	breast:
6	chr12:123318351..123322726-chr12:123344658..123350717,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182196	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000130783	Chromatin interaction
ENSG00000139722	Chromatin interaction
ENSG00000139726	Chromatin interaction
ENSG00000090975	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000256152	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10773627	0.90[ASN][1000 genomes]
rs10773657	0.90[ASN][1000 genomes]
rs10847826	0.90[ASN][1000 genomes]
rs10847869	0.90[ASN][1000 genomes]
rs11060064	0.86[ASN][1000 genomes]
rs11060065	0.86[ASN][1000 genomes]
rs11060208	0.91[ASN][1000 genomes]
rs11060209	0.98[ASN][1000 genomes]
rs12298151	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12298664	1.00[ASN][1000 genomes]
rs12299742	0.98[ASN][1000 genomes]
rs12313006	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12314494	1.00[ASN][1000 genomes]
rs12314544	1.00[ASN][1000 genomes]
rs12319654	1.00[ASN][1000 genomes]
rs12321131	0.86[ASN][1000 genomes]
rs12426809	0.90[ASN][1000 genomes]
rs1532835	0.88[ASN][1000 genomes]
rs1587856	0.80[ASN][1000 genomes]
rs1671685	1.00[ASN][1000 genomes]
rs1696326	1.00[ASN][1000 genomes]
rs1696349	1.00[ASN][1000 genomes]
rs1799618	1.00[ASN][1000 genomes]
rs1979236	1.00[ASN][1000 genomes]
rs1979237	1.00[ASN][1000 genomes]
rs2135014	0.88[ASN][1000 genomes]
rs2271051	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2292131	1.00[ASN][1000 genomes]
rs2292132	0.88[ASN][1000 genomes]
rs2292134	0.86[ASN][1000 genomes]
rs2292135	0.84[ASN][1000 genomes]
rs2292136	0.82[ASN][1000 genomes]
rs2292138	0.80[ASN][1000 genomes]
rs2292139	0.83[ASN][1000 genomes]
rs2343108	0.88[ASN][1000 genomes]
rs2343109	0.80[ASN][1000 genomes]
rs2343685	0.90[ASN][1000 genomes]
rs2649908	0.99[ASN][1000 genomes]
rs2649909	1.00[ASN][1000 genomes]
rs2880678	0.90[ASN][1000 genomes]
rs3817094	0.87[ASN][1000 genomes]
rs3852536	0.86[ASN][1000 genomes]
rs4759355	0.94[ASN][1000 genomes]
rs4759389	0.90[ASN][1000 genomes]
rs4759392	0.81[ASN][1000 genomes]
rs56272219	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58182048	0.86[ASN][1000 genomes]
rs59192320	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59922385	1.00[ASN][1000 genomes]
rs60308342	0.97[ASN][1000 genomes]
rs7138398	0.80[ASN][1000 genomes]
rs7294991	0.81[ASN][1000 genomes]
rs7303024	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309225	0.81[ASN][1000 genomes]
rs73421642	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs735378	1.00[ASN][1000 genomes]
rs7398546	0.84[ASN][1000 genomes]
rs754080	1.00[ASN][1000 genomes]
rs897385	0.80[ASN][1000 genomes]
rs897386	0.80[ASN][1000 genomes]
rs897391	0.90[ASN][1000 genomes]
rs897392	0.90[ASN][1000 genomes]
rs897393	0.90[ASN][1000 genomes]
rs921808	0.88[ASN][1000 genomes]
rs936083	0.82[ASN][1000 genomes]
rs937520	0.98[ASN][1000 genomes]
rs937766	0.88[ASN][1000 genomes]
rs9788290	0.86[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	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:44 , 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	chr12:123318200-123318800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:123318200-123318800	Enhancers	Fetal Brain Female	brain
32	chr12:123318400-123318800	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr12:123318400-123318800	Weak transcription	Brain Anterior Caudate	brain
34	chr12:123318400-123319000	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr12:123318600-123318800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:123318600-123318800	Enhancers	Primary hematopoietic stem cells	blood
37	chr12:123318600-123318800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr12:123318600-123318800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:123318600-123318800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:123318600-123318800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:123318600-123318800	Active TSS	Brain Germinal Matrix	brain
42	chr12:123318600-123318800	Enhancers	Hela-S3	cervix
43	chr12:123318600-123318800	Enhancers	HSMMtube	muscle
44	chr12:123318600-123319000	Enhancers	Stomach Mucosa	stomach

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