Variant report

Variant	rs2078398
Chromosome Location	chr12:65068770-65068771
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:65017129..65019171-chr12:65067339..65069384,2	MCF-7	breast:
2	chr12:65002496..65005791-chr12:65064142..65070485,7	K562	blood:
3	chr12:65002391..65005791-chr12:65064142..65070932,8	K562	blood:
4	chr12:65057089..65059897-chr12:65066585..65070276,3	K562	blood:
5	chr12:65057089..65063734-chr12:65063788..65069344,8	K562	blood:
6	chr12:65011593..65014021-chr12:65067404..65069519,2	K562	blood:

Variant related genes	Relation type
ENSG00000256670	Chromatin interaction
ENSG00000153179	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1008159	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1008160	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175470	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11175471	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11175476	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11175478	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11175481	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11175497	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11175509	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11837759	0.85[CEU][hapmap]
rs12230536	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12814316	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12816847	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12824246	0.91[ASN][1000 genomes]
rs12829878	0.85[CEU][hapmap]
rs12830436	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12831875	0.85[CEU][hapmap]
rs12833931	0.86[EUR][1000 genomes]
rs17223244	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17223377	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17223391	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17823442	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs35512928	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35674528	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35705715	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35860561	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7303641	0.81[EUR][1000 genomes]
rs7304648	0.81[EUR][1000 genomes]
rs7959471	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv899209	chr12:65068686-65184236	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65058400-65069600	Enhancers	Small Intestine	intestine
2	chr12:65058800-65070000	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr12:65059400-65068800	Enhancers	Fetal Intestine Large	intestine
4	chr12:65060000-65073400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:65060200-65069200	Weak transcription	Osteobl	bone
6	chr12:65061800-65069800	Enhancers	Fetal Intestine Small	intestine
7	chr12:65062600-65069600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:65062600-65070000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:65062600-65071600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:65063000-65069600	Enhancers	Pancreas	Pancrea
11	chr12:65063000-65070000	Enhancers	Lung	lung
12	chr12:65063000-65071400	Enhancers	Left Ventricle	heart
13	chr12:65063400-65068800	Enhancers	Placenta	Placenta
14	chr12:65063600-65069600	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr12:65063600-65071400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr12:65063600-65073400	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr12:65064000-65068800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:65064000-65069800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:65064000-65070600	Enhancers	Colonic Mucosa	Colon
20	chr12:65064000-65073400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:65064000-65073400	Weak transcription	Fetal Brain Male	brain
22	chr12:65064000-65076000	Enhancers	Fetal Thymus	thymus
23	chr12:65064000-65078200	Enhancers	Primary B cells from peripheral blood	blood
24	chr12:65064400-65070200	Enhancers	Primary hematopoietic stem cells	blood
25	chr12:65065000-65069400	Weak transcription	NHDF-Ad	bronchial
26	chr12:65065200-65069400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:65065600-65069800	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr12:65065600-65072200	Enhancers	Thymus	Thymus
29	chr12:65065800-65069400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:65065800-65069600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:65066000-65068800	Enhancers	HepG2	liver
32	chr12:65066000-65070000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:65066000-65078600	Enhancers	Spleen	Spleen
34	chr12:65066200-65069800	Enhancers	Right Ventricle	heart
35	chr12:65066400-65068800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:65066400-65068800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:65066400-65069000	Enhancers	Fetal Stomach	stomach
38	chr12:65066400-65069600	Enhancers	Right Atrium	heart
39	chr12:65066400-65069800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:65066600-65068800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr12:65066600-65068800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr12:65066600-65069800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr12:65066800-65068800	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr12:65066800-65069400	Enhancers	Hela-S3	cervix
45	chr12:65066800-65073200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:65066800-65073600	Weak transcription	Esophagus	oesophagus
47	chr12:65067000-65070000	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr12:65067000-65073200	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr12:65067000-65073200	Weak transcription	HSMM	muscle
50	chr12:65067000-65075000	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links