Variant report

Variant	rs56289822
Chromosome Location	chr2:55768538-55768539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs55715440	1.00[EUR][1000 genomes]
rs56062543	1.00[AMR][1000 genomes]
rs56088561	1.00[AMR][1000 genomes]
rs56296556	1.00[EUR][1000 genomes]
rs6720102	1.00[AMR][1000 genomes]
rs72803505	1.00[AMR][1000 genomes]
rs72803524	1.00[EUR][1000 genomes]
rs72803533	1.00[AMR][1000 genomes]
rs72803575	1.00[EUR][1000 genomes]
rs72803593	1.00[AMR][1000 genomes]
rs72805477	1.00[AMR][1000 genomes]
rs72805485	1.00[EUR][1000 genomes]
rs72805497	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72807607	1.00[EUR][1000 genomes]
rs72812147	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72812149	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72812151	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55747800-55784000	Weak transcription	Esophagus	oesophagus
2	chr2:55748000-55784000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:55748000-55788000	Weak transcription	Colonic Mucosa	Colon
4	chr2:55748000-55793800	Weak transcription	Psoas Muscle	Psoas
5	chr2:55748200-55769600	Weak transcription	Small Intestine	intestine
6	chr2:55748200-55769600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr2:55748200-55772000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:55748200-55773000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:55748200-55775800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:55748200-55777400	Weak transcription	NHLF	lung
11	chr2:55748200-55778800	Weak transcription	Fetal Heart	heart
12	chr2:55748200-55782400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr2:55748400-55772200	Weak transcription	HMEC	breast
14	chr2:55748600-55770000	Weak transcription	Dnd41	blood
15	chr2:55750000-55775400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:55752600-55788200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
18	chr2:55753200-55772400	Weak transcription	HepG2	liver
19	chr2:55753400-55772200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:55753600-55786600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:55753800-55768800	Weak transcription	Placenta	Placenta
22	chr2:55754000-55774600	Weak transcription	Spleen	Spleen
23	chr2:55754000-55784000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:55754200-55772400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:55754400-55772200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:55754400-55783000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:55758000-55771400	Weak transcription	NH-A	brain
28	chr2:55758200-55770800	Weak transcription	Brain Substantia Nigra	brain
29	chr2:55758200-55781200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:55758200-55783800	Weak transcription	Gastric	stomach
31	chr2:55758200-55784000	Weak transcription	Pancreas	Pancrea
32	chr2:55758400-55774000	Weak transcription	Hela-S3	cervix
33	chr2:55758400-55776000	Weak transcription	HUVEC	blood vessel
34	chr2:55758600-55784000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr2:55759000-55769800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:55759200-55769600	Weak transcription	Colon Smooth Muscle	Colon
37	chr2:55759200-55772400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr2:55759600-55773800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:55760800-55788000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:55761000-55788200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:55761200-55777200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:55761400-55781600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:55762000-55772200	Weak transcription	Brain Germinal Matrix	brain
44	chr2:55762000-55783800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:55762200-55771200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr2:55762200-55771200	Weak transcription	Lung	lung
47	chr2:55762200-55771800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr2:55762200-55773000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:55762200-55782600	Weak transcription	NHEK	skin
50	chr2:55762200-55784000	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links