Variant report

Variant	rs404598
Chromosome Location	chr5:101584499-101584500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10041806	0.86[CEU][hapmap];0.87[JPT][hapmap]
rs10055023	0.88[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs10057126	0.82[CEU][hapmap]
rs10062613	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs10065821	0.85[JPT][hapmap]
rs10069193	0.83[CEU][hapmap]
rs10069466	0.83[AMR][1000 genomes]
rs10223273	0.85[JPT][hapmap]
rs10479216	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs1376894	0.88[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs1376898	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs1376910	0.88[GIH][hapmap];0.85[JPT][hapmap]
rs1376911	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs1452059	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1542296	0.88[CEU][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs1545487	0.86[GIH][hapmap];0.85[JPT][hapmap]
rs1545488	0.88[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs1562960	0.88[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs1562961	0.85[JPT][hapmap]
rs17273466	0.80[CEU][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap]
rs1901512	0.85[JPT][hapmap]
rs1901521	0.85[JPT][hapmap]
rs1901522	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs2060833	0.88[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap]
rs2084826	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs2123133	0.88[GIH][hapmap];0.85[JPT][hapmap]
rs2123135	0.83[CEU][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap]
rs2400795	0.88[GIH][hapmap];0.85[JPT][hapmap]
rs2400797	0.85[JPT][hapmap]
rs2400801	0.85[JPT][hapmap]
rs2548725	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2600826	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2600831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3096214	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3114661	0.96[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3114665	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs384615	0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs386464	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs416332	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4703226	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs6596482	0.88[GIH][hapmap];0.85[JPT][hapmap]
rs6596493	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs6596495	0.84[JPT][hapmap]
rs6871070	0.85[JPT][hapmap]
rs6871966	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs6873738	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs6877722	0.85[JPT][hapmap]
rs6878190	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6885800	0.86[CEU][hapmap];0.83[JPT][hapmap]
rs6890130	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs6895200	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs709372	0.96[CEU][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7715217	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs7719316	0.91[CEU][hapmap];0.94[JPT][hapmap]
rs7721084	0.82[JPT][hapmap]
rs7731256	0.85[JPT][hapmap]
rs7733253	0.88[CEU][hapmap];0.89[JPT][hapmap]
rs7734926	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7736579	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs7737204	0.87[CEU][hapmap];0.84[JPT][hapmap]
rs841921	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs841923	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs841924	0.81[JPT][hapmap]
rs841925	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs841933	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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	nsv1022551	chr5:101366177-101649643	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv882505	chr5:101397849-101652251	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1028787	chr5:101432086-101718569	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv817537	chr5:101489151-101992104	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1016176	chr5:101534391-102333606	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv537831	chr5:101534391-102333606	Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 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	chr5:101567400-101585000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr5:101568200-101599000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:101568800-101584800	Weak transcription	Fetal Intestine Large	intestine
4	chr5:101568800-101598200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr5:101570200-101599600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr5:101570800-101587800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:101578200-101585000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr5:101578200-101598200	Weak transcription	Pancreas	Pancrea
9	chr5:101579200-101598200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:101579800-101598600	Weak transcription	Lung	lung
11	chr5:101580000-101604400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:101582200-101585200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr5:101583000-101591400	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links