Variant report

Variant	rs2820
Chromosome Location	chr2:20549434-20549435
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20525204..20529381-chr2:20546645..20551782,7	K562	blood:
2	chr2:20099437..20102980-chr2:20547960..20551663,4	K562	blood:
3	chr2:20549379..20553875-chr2:20644345..20648832,13	MCF-7	breast:
4	chr2:20523318..20529381-chr2:20544822..20552572,11	K562	blood:
5	chr2:20548847..20552407-chr2:20645405..20649585,5	MCF-7	breast:
6	chr2:20549000..20550935-chr2:20649579..20652329,2	MCF-7	breast:
7	chr11:65685171..65687731-chr2:20547276..20549842,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271991	Chromatin interaction
ENSG00000175550	Chromatin interaction
ENSG00000175573	Chromatin interaction
ENSG00000228950	Chromatin interaction
ENSG00000183891	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000055917	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1043400	0.87[CEU][hapmap];0.81[TSI][hapmap]
rs10460445	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10460449	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10460450	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10495704	0.82[CEU][hapmap]
rs11096654	0.87[EUR][1000 genomes]
rs11096659	0.87[EUR][1000 genomes]
rs11888357	0.87[CEU][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11895228	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11896241	0.81[ASW][hapmap];0.95[CEU][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11898408	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11900127	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11903745	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12465832	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12473500	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12474897	0.87[EUR][1000 genomes]
rs12478265	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17612703	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2015110	0.82[JPT][hapmap]
rs2080190	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2110410	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2348703	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3796066	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs3821218	1.00[ASW][hapmap];0.83[CEU][hapmap];0.80[TSI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6748274	0.87[CEU][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72785295	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72785297	0.80[EUR][1000 genomes]
rs72785298	0.81[EUR][1000 genomes]
rs72785300	0.81[EUR][1000 genomes]
rs72787406	0.87[EUR][1000 genomes]
rs72787409	0.87[EUR][1000 genomes]
rs72787411	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72787415	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72787433	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72787499	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72787500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72787501	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72788905	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72788906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741188	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7558385	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7579571	0.87[EUR][1000 genomes]

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20545200-20549600	Weak transcription	Esophagus	oesophagus
2	chr2:20546800-20549800	Weak transcription	Spleen	Spleen
3	chr2:20547400-20550000	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr2:20547600-20551800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:20547800-20549600	Weak transcription	Small Intestine	intestine
6	chr2:20547800-20550000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:20547800-20551400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:20548200-20549600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
9	chr2:20548200-20549600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
10	chr2:20548200-20549600	Flanking Active TSS	Liver	Liver
11	chr2:20548200-20549600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr2:20548200-20549800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr2:20548200-20549800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:20548200-20549800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr2:20548200-20549800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr2:20548200-20549800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:20548200-20549800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:20548200-20550800	Active TSS	Stomach Smooth Muscle	stomach
19	chr2:20548400-20549600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:20548400-20549800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:20548400-20549800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr2:20548400-20551000	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr2:20548400-20551000	Active TSS	Colonic Mucosa	Colon
24	chr2:20548400-20551000	Active TSS	Fetal Intestine Large	intestine
25	chr2:20548400-20551200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:20548400-20551600	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr2:20548600-20549800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr2:20548600-20549800	Weak transcription	Pancreas	Pancrea
29	chr2:20548600-20550800	Active TSS	Placenta	Placenta
30	chr2:20548600-20551000	Active TSS	H1 Cell Line	embryonic stem cell
31	chr2:20548600-20551000	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr2:20548600-20551000	Active TSS	A549	lung
33	chr2:20548600-20551000	Active TSS	K562	blood
34	chr2:20548600-20551200	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr2:20548600-20551200	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr2:20548600-20551200	Active TSS	Fetal Intestine Small	intestine
37	chr2:20548600-20551200	Active TSS	Fetal Thymus	thymus
38	chr2:20548600-20551400	Active TSS	Right Ventricle	heart
39	chr2:20548600-20551600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:20548600-20551600	Active TSS	Ovary	ovary
41	chr2:20548600-20551800	Active TSS	Thymus	Thymus
42	chr2:20548800-20549600	Weak transcription	Lung	lung
43	chr2:20548800-20549600	Enhancers	Placenta Amnion	Placenta Amnion
44	chr2:20548800-20549600	Flanking Active TSS	Rectal Smooth Muscle	rectum
45	chr2:20548800-20549600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:20548800-20549800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:20548800-20549800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:20548800-20549800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:20548800-20550000	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr2:20548800-20550000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links