Variant report

Variant	rs6826467
Chromosome Location	chr4:54139334-54139335
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10013573	0.85[CHB][hapmap]
rs1014056	0.85[CHB][hapmap];0.82[CHD][hapmap];0.84[MEX][hapmap]
rs10517291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10517292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10517296	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs11133267	0.85[CHB][hapmap];0.82[CHD][hapmap];0.84[MEX][hapmap]
rs11929903	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.85[AMR][1000 genomes]
rs11930070	1.00[CEU][hapmap]
rs11939189	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap]
rs11947322	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11947928	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12108246	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.85[AMR][1000 genomes]
rs12499016	1.00[CHB][hapmap]
rs12499401	0.85[CHB][hapmap]
rs12499731	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12500564	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12505661	0.85[AMR][1000 genomes]
rs12512748	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13120051	0.85[CHB][hapmap]
rs1351514	0.85[CHB][hapmap];0.85[CHD][hapmap];0.82[MEX][hapmap]
rs17082453	0.85[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs17082476	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs17082504	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.85[AMR][1000 genomes]
rs17082549	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17082565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17082579	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17082581	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1987028	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs2001881	0.85[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs2128103	0.85[CHB][hapmap];0.89[CHD][hapmap];0.84[MEX][hapmap]
rs34019927	0.82[AMR][1000 genomes]
rs35225781	0.85[CHB][hapmap];0.82[CHD][hapmap];0.84[MEX][hapmap]
rs35784764	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3817270	0.85[CHB][hapmap]
rs4299650	0.85[AMR][1000 genomes]
rs4385131	1.00[CEU][hapmap];0.91[JPT][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4419530	0.85[AMR][1000 genomes]
rs4421047	0.93[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes]
rs4529117	0.85[AMR][1000 genomes]
rs4864451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4864452	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864453	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864454	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864753	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6420001	0.85[CHB][hapmap];0.82[CHD][hapmap];0.84[MEX][hapmap]
rs6554095	0.85[CHB][hapmap]
rs6554096	0.85[CHB][hapmap]
rs6830879	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6854446	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72498838	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73147378	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73147396	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73149212	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs751265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7664488	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7664645	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7684450	0.85[CHB][hapmap]
rs7687029	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7688646	0.93[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.85[AMR][1000 genomes]
rs7696426	0.85[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs9762074	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9992820	0.85[CHB][hapmap];0.82[CHD][hapmap];0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997614	chr4:54086727-54150632	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1008593	chr4:54120297-54207769	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv2763360	chr4:54123894-54153814	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54114400-54139600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr4:54114400-54144000	Weak transcription	Liver	Liver
3	chr4:54122200-54139800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr4:54126800-54141400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:54127600-54153000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:54129600-54141400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr4:54129600-54154600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr4:54129800-54145200	Weak transcription	Fetal Lung	lung
9	chr4:54130400-54143400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:54130400-54148600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:54130400-54150400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:54130600-54148200	Weak transcription	Fetal Intestine Small	intestine
13	chr4:54131000-54145800	Weak transcription	Primary B cells from cord blood	blood
14	chr4:54133000-54141400	Weak transcription	Placenta	Placenta
15	chr4:54133200-54144600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr4:54133600-54139600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:54133800-54139600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:54134800-54140000	Weak transcription	NHDF-Ad	bronchial
19	chr4:54134800-54151000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:54134800-54154200	Weak transcription	NHLF	lung
21	chr4:54135000-54145600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:54135000-54145800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr4:54135000-54151200	Weak transcription	Left Ventricle	heart
24	chr4:54135200-54140800	Weak transcription	Pancreas	Pancrea
25	chr4:54135200-54142600	Weak transcription	GM12878-XiMat	blood
26	chr4:54135200-54144000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:54135200-54148200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:54135200-54151800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:54135200-54154600	Weak transcription	Primary T cells from cord blood	blood
30	chr4:54135400-54146000	Weak transcription	Fetal Stomach	stomach
31	chr4:54135400-54152200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:54135400-54153000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links