Variant report

Variant	rs952188
Chromosome Location	chr6:54668224-54668225
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54666819..54668967-chr6:54700012..54702691,2	MCF-7	breast:
2	chr6:54667811..54670876-chr6:54711137..54713039,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10080497	0.91[ASN][1000 genomes]
rs10080987	0.91[ASN][1000 genomes]
rs10807479	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10807481	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10948855	0.94[ASN][1000 genomes]
rs12197981	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1393777	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1503133	0.84[MEX][hapmap]
rs1503151	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1503152	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1566753	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1604672	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1812584	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1976537	0.83[ASN][1000 genomes]
rs1976538	0.83[ASN][1000 genomes]
rs2397168	0.83[ASN][1000 genomes]
rs2397169	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2397170	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2397171	0.84[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap]
rs35839415	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3929470	0.84[ASN][1000 genomes]
rs4516942	0.84[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs4712072	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4712073	0.94[ASN][1000 genomes]
rs4712074	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57506664	0.84[EUR][1000 genomes]
rs6901946	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6901963	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6916633	0.83[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs6916818	0.94[ASN][1000 genomes]
rs6919743	0.94[ASN][1000 genomes]
rs6926214	0.91[ASN][1000 genomes]
rs6934377	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7738681	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7749110	0.94[ASN][1000 genomes]
rs7751955	0.81[CEU][hapmap]
rs7752214	0.80[MEX][hapmap]
rs7760610	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7760890	0.91[ASN][1000 genomes]
rs7761084	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7762606	0.84[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.88[ASN][1000 genomes]
rs9349732	0.91[ASN][1000 genomes]
rs9349733	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9367591	0.91[ASN][1000 genomes]
rs9370328	0.91[ASN][1000 genomes]
rs9395997	0.96[ASN][1000 genomes]
rs9464137	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9464145	0.87[ASW][hapmap];0.91[LWK][hapmap]
rs9475007	0.90[ASN][1000 genomes]
rs9475010	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9475014	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs965009	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs973020	0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54666200-54669200	Enhancers	Fetal Intestine Large	intestine
2	chr6:54666400-54668400	Enhancers	NHLF	lung
3	chr6:54666600-54668400	Enhancers	Hela-S3	cervix
4	chr6:54666600-54668400	Enhancers	NHEK	skin
5	chr6:54666600-54669400	Weak transcription	HSMMtube	muscle
6	chr6:54667000-54668600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:54667200-54668800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:54667200-54668800	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr6:54667600-54668400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr6:54667800-54668400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:54667800-54668400	Enhancers	Placenta Amnion	Placenta Amnion
12	chr6:54667800-54669000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr6:54667800-54670800	Enhancers	Fetal Intestine Small	intestine
14	chr6:54668000-54668400	Enhancers	Fetal Heart	heart
15	chr6:54668200-54668600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:54668200-54668800	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr6:54668200-54669400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:54668200-54670200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr6:54668200-54670400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:54668200-54670400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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