Variant report

Variant	rs4959998
Chromosome Location	chr6:4491493-4491494
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4490287..4491939-chr6:4601250..4603632,2	MCF-7	breast:
2	chr6:4488176..4491651-chr6:4775983..4779929,5	MCF-7	breast:
3	chr6:4489721..4491825-chr6:4493437..4495768,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153046	Chromatin interaction
ENSG00000260673	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1009602	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1009603	0.89[ASN][1000 genomes]
rs1009604	0.89[ASN][1000 genomes]
rs1011088	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap]
rs1011089	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11752793	0.85[AMR][1000 genomes]
rs1265245	0.90[ASN][1000 genomes]
rs1265250	0.92[ASN][1000 genomes]
rs1265256	0.83[ASN][1000 genomes]
rs2021989	0.82[ASN][1000 genomes]
rs2150231	0.92[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2181015	0.83[CHB][hapmap];0.87[CHD][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes]
rs2875945	0.82[ASN][1000 genomes]
rs3929704	0.83[ASN][1000 genomes]
rs4246070	0.81[ASN][1000 genomes]
rs4959298	0.82[ASN][1000 genomes]
rs4959299	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4959300	0.85[AMR][1000 genomes]
rs4959301	0.80[CHD][hapmap]
rs4959987	0.81[ASN][1000 genomes]
rs4959993	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap]
rs4959995	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs4959997	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57361712	0.85[AMR][1000 genomes]
rs60221507	0.82[ASN][1000 genomes]
rs61449781	0.85[AMR][1000 genomes]
rs62384876	0.84[ASN][1000 genomes]
rs6914063	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap]
rs7450179	0.81[ASN][1000 genomes]
rs7452972	0.81[ASN][1000 genomes]
rs7453574	0.81[ASN][1000 genomes]
rs911566	0.81[ASN][1000 genomes]
rs911567	0.81[ASN][1000 genomes]
rs9378879	0.81[ASN][1000 genomes]
rs9378880	0.81[ASN][1000 genomes]
rs9378881	0.81[ASN][1000 genomes]
rs9378882	0.82[ASN][1000 genomes]
rs9378883	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9392603	0.81[ASN][1000 genomes]
rs9405247	0.82[ASN][1000 genomes]
rs9405248	0.82[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	nsv1021743	chr6:4382308-4494308	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv538111	chr6:4382308-4494308	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3421990	chr6:4446933-4659639	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv830576	chr6:4447554-4610604	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv970369	chr6:4481968-4554947	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4490000-4492400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:4490400-4492600	Enhancers	Placenta	Placenta
3	chr6:4491000-4492000	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links