Variant report

Variant	rs1458239
Chromosome Location	chr4:69819625-69819626
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10000481	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10004381	1.00[EUR][1000 genomes]
rs10005280	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10014997	1.00[EUR][1000 genomes]
rs10015332	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10018123	1.00[EUR][1000 genomes]
rs10030582	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10030703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1020766	0.82[ASN][1000 genomes]
rs10903222	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1117530	1.00[EUR][1000 genomes]
rs1117531	1.00[EUR][1000 genomes]
rs11728297	0.91[ASN][1000 genomes]
rs1303726	1.00[EUR][1000 genomes]
rs13113179	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13148459	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13148751	0.88[ASN][1000 genomes]
rs1379814	1.00[EUR][1000 genomes]
rs1379815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1598901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1902924	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2018001	0.89[ASN][1000 genomes]
rs2125306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331566	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2331575	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2331576	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2877423	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3828503	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3966087	1.00[EUR][1000 genomes]
rs4391113	0.88[ASN][1000 genomes]
rs4419538	0.89[ASN][1000 genomes]
rs4532300	0.88[ASN][1000 genomes]
rs4643882	0.89[ASN][1000 genomes]
rs4694492	0.82[ASN][1000 genomes]
rs6812386	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6814321	1.00[EUR][1000 genomes]
rs6818594	0.91[ASN][1000 genomes]
rs6851476	0.91[ASN][1000 genomes]
rs6858371	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7657317	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7659264	0.88[ASN][1000 genomes]
rs7659867	0.91[ASN][1000 genomes]
rs7664636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7672933	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7678708	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7688541	1.00[EUR][1000 genomes]
rs9329038	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005513	chr4:69446718-69890307	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv999654	chr4:69661415-70132110	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv3420586	chr4:69680878-70322918	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	esv3398036	chr4:69700493-69841391	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1067773	chr4:69718248-70715727	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	esv3468151	chr4:69718675-70322776	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	esv3468153	chr4:69718675-70322776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv436447	chr4:69743339-69851390	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv967758	chr4:69780530-69870183	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv829962	chr4:69786869-69910283	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv10519	chr4:69816500-69835939	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69815200-69825600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:69817200-69819800	Enhancers	HepG2	liver
3	chr4:69817600-69820600	Enhancers	Fetal Intestine Large	intestine
4	chr4:69817600-69820600	Enhancers	Fetal Intestine Small	intestine
5	chr4:69817800-69820400	Enhancers	Duodenum Mucosa	Duodenum
6	chr4:69818200-69820000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:69818600-69819800	Weak transcription	Liver	Liver
8	chr4:69818600-69820200	Enhancers	Fetal Heart	heart
9	chr4:69818600-69820200	Enhancers	Stomach Mucosa	stomach
10	chr4:69818800-69820200	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr4:69819600-69820200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:69819600-69820200	Enhancers	Pancreas	Pancrea
13	chr4:69819600-69820400	Enhancers	Small Intestine	intestine

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