Variant report

Variant	rs2594283
Chromosome Location	chr4:87776185-87776186
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87769723..87774057-chr4:87775131..87777452,3	MCF-7	breast:
2	chr4:87755836..87758517-chr4:87776083..87778116,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145283	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10011798	0.94[EUR][1000 genomes]
rs10015121	0.94[EUR][1000 genomes]
rs10021020	0.95[EUR][1000 genomes]
rs10034336	0.93[EUR][1000 genomes]
rs11097123	0.86[EUR][1000 genomes]
rs11097125	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12503045	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12507165	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12641570	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13120981	0.95[EUR][1000 genomes]
rs1374935	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1868244	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2012345	0.86[ASN][1000 genomes]
rs2121871	0.95[EUR][1000 genomes]
rs2594274	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2594284	0.84[AFR][1000 genomes]
rs2705626	0.84[AFR][1000 genomes]
rs2705629	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28446826	0.82[EUR][1000 genomes]
rs2904148	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2904150	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35428486	0.94[EUR][1000 genomes]
rs4235082	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55889191	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56062410	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67758970	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6823051	0.95[EUR][1000 genomes]
rs6843070	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6846822	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87769600-87776800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:87769800-87778600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:87770200-87776800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:87770400-87778600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:87771200-87776200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:87771600-87776200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:87771600-87776200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:87771600-87776800	Weak transcription	Right Atrium	heart
9	chr4:87771600-87785600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr4:87771800-87776200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:87771800-87776400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:87771800-87776400	Weak transcription	NHEK	skin
13	chr4:87771800-87776800	Weak transcription	Left Ventricle	heart
14	chr4:87771800-87776800	Weak transcription	Hela-S3	cervix
15	chr4:87774800-87776600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:87775800-87779200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links