Variant report

Variant	rs4959994
Chromosome Location	chr6:4482625-4482626
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	chr6:4479237..4481357-chr6:4482342..4483965,2	MCF-7	breast:
2	chr6:4481267..4483998-chr6:4490747..4493178,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260239	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1009602	0.82[ASN][1000 genomes]
rs1009603	0.88[ASN][1000 genomes]
rs1009604	0.88[ASN][1000 genomes]
rs1011087	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1011088	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1011089	0.99[ASN][1000 genomes]
rs12525331	0.90[ASN][1000 genomes]
rs1265245	0.80[ASN][1000 genomes]
rs1265250	0.86[ASN][1000 genomes]
rs1265256	0.82[ASN][1000 genomes]
rs1265259	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1265260	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13195445	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1571630	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2021989	0.93[ASN][1000 genomes]
rs2150231	0.82[ASN][1000 genomes]
rs2875945	0.93[ASN][1000 genomes]
rs3929704	0.82[ASN][1000 genomes]
rs4246070	0.92[ASN][1000 genomes]
rs4959295	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959296	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959297	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959298	0.93[ASN][1000 genomes]
rs4959987	0.91[ASN][1000 genomes]
rs4959989	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959990	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959991	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959992	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959993	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4959995	0.81[ASN][1000 genomes]
rs60221507	0.93[ASN][1000 genomes]
rs62384876	0.81[ASN][1000 genomes]
rs6914063	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6930327	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7450179	0.92[ASN][1000 genomes]
rs7452972	0.92[ASN][1000 genomes]
rs7453574	0.92[ASN][1000 genomes]
rs911565	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs911566	0.92[ASN][1000 genomes]
rs911567	0.92[ASN][1000 genomes]
rs9378879	0.92[ASN][1000 genomes]
rs9378880	0.92[ASN][1000 genomes]
rs9378881	0.92[ASN][1000 genomes]
rs9378882	0.93[ASN][1000 genomes]
rs9378883	0.85[ASN][1000 genomes]
rs9392053	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9392602	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9392603	0.92[ASN][1000 genomes]
rs9405247	0.93[ASN][1000 genomes]
rs9405248	0.93[ASN][1000 genomes]
rs9405748	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9502189	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9504122	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9504123	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9504124	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[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:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4480400-4483000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:4480600-4482800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
3	chr6:4480600-4483200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:4480600-4483400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:4481600-4484400	Weak transcription	Right Atrium	heart
6	chr6:4482200-4482800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:4482600-4485200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links