Variant report

Variant	rs3909458
Chromosome Location	chr5:59835068-59835069
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:59831215..59833995-chr5:59834537..59838360,3	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10516154	1.00[ASN][1000 genomes]
rs11957512	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960912	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16878190	1.00[ASN][1000 genomes]
rs16878304	1.00[ASN][1000 genomes]
rs2061252	1.00[ASN][1000 genomes]
rs2061254	1.00[ASN][1000 genomes]
rs2409763	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2441051	1.00[ASN][1000 genomes]
rs2441052	1.00[ASN][1000 genomes]
rs2591635	1.00[ASN][1000 genomes]
rs2606688	1.00[ASN][1000 genomes]
rs286150	1.00[ASN][1000 genomes]
rs286151	1.00[ASN][1000 genomes]
rs286152	1.00[ASN][1000 genomes]
rs286157	1.00[ASN][1000 genomes]
rs286159	1.00[ASN][1000 genomes]
rs3857237	1.00[ASN][1000 genomes]
rs3887175	1.00[ASN][1000 genomes]
rs6872509	1.00[ASN][1000 genomes]
rs73110509	0.96[EUR][1000 genomes]
rs7728865	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737238	0.93[EUR][1000 genomes]
rs9686946	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv598297	chr5:59734004-59862453	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59828000-59837000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:59830000-59835200	Weak transcription	HepG2	liver
3	chr5:59830400-59835400	Weak transcription	Brain Hippocampus Middle	brain
4	chr5:59833400-59838200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr5:59833400-59838800	Enhancers	Primary T cells from cord blood	blood
6	chr5:59833800-59835400	Enhancers	Primary B cells from cord blood	blood
7	chr5:59834000-59839200	Enhancers	Primary B cells from peripheral blood	blood
8	chr5:59834200-59838200	Enhancers	Brain Angular Gyrus	brain
9	chr5:59834400-59835600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr5:59834600-59835800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:59834600-59836200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr5:59834600-59838200	Enhancers	Brain Substantia Nigra	brain
13	chr5:59834800-59836600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:59835000-59837000	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links