Variant report

Variant	rs256956
Chromosome Location	chr5:114877022-114877023
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12187973	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs171774	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs187682	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2169771	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2546484	0.83[CEU][hapmap]
rs2546486	0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2546487	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2559990	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs256938	0.85[CEU][hapmap]
rs256940	0.86[CHB][hapmap]
rs256943	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs256944	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs256945	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs256959	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs256964	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs256968	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs256976	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs256980	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs256984	0.84[EUR][1000 genomes]
rs256986	0.84[EUR][1000 genomes]
rs256994	0.82[ASN][1000 genomes]
rs256996	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs256997	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs372702	0.83[CEU][hapmap]
rs387718	0.82[ASN][1000 genomes]
rs415577	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs6893854	0.80[CEU][hapmap]
rs6894123	0.80[CEU][hapmap]
rs813761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv830455	chr5:114761542-114938284	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1032234	chr5:114785557-114911527	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1796164	chr5:114854685-114936768	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv965571	chr5:114874943-114878934	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114857800-114877200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:114858600-114878800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:114860800-114877200	Weak transcription	Colonic Mucosa	Colon
4	chr5:114861000-114878600	Weak transcription	Pancreas	Pancrea
5	chr5:114861000-114878800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:114861000-114878800	Weak transcription	Spleen	Spleen
7	chr5:114861200-114878600	Weak transcription	Esophagus	oesophagus
8	chr5:114861400-114877200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:114863600-114878600	Weak transcription	Gastric	stomach
10	chr5:114868400-114878000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:114870000-114877400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
12	chr5:114871200-114879200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:114872200-114877400	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr5:114872600-114879400	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
15	chr5:114873400-114877200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:114873800-114877400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
17	chr5:114874000-114878000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr5:114874000-114878200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr5:114874000-114879200	Transcr. at gene 5' and 3'	Dnd41	blood
20	chr5:114874200-114881200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:114874400-114878000	Weak transcription	Stomach Mucosa	stomach
22	chr5:114874400-114878800	Active TSS	Stomach Smooth Muscle	stomach
23	chr5:114874600-114878800	Active TSS	Right Ventricle	heart
24	chr5:114874800-114877200	Weak transcription	Aorta	Aorta
25	chr5:114875400-114877200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr5:114875400-114877200	Transcr. at gene 5' and 3'	Osteobl	bone
27	chr5:114875400-114877400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr5:114875400-114877400	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
29	chr5:114875400-114877800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:114875400-114878600	Active TSS	Brain Germinal Matrix	brain
31	chr5:114875600-114877200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr5:114875600-114877600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:114875600-114878800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr5:114875600-114878800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
35	chr5:114875600-114878800	Active TSS	Psoas Muscle	Psoas
36	chr5:114875600-114879000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:114875600-114879000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:114875600-114880000	Active TSS	Right Atrium	heart
39	chr5:114875600-114881000	Active TSS	Fetal Brain Female	brain
40	chr5:114875600-114881200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:114875800-114877200	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr5:114875800-114877400	Transcr. at gene 5' and 3'	Fetal Lung	lung
43	chr5:114875800-114878600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:114875800-114879000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
45	chr5:114875800-114879000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
46	chr5:114875800-114879200	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
47	chr5:114876000-114877200	Weak transcription	Left Ventricle	heart
48	chr5:114876000-114877200	Weak transcription	Small Intestine	intestine
49	chr5:114876000-114877400	Weak transcription	Placenta	Placenta
50	chr5:114876000-114878000	Active TSS	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links