Variant report

Variant	rs2642299
Chromosome Location	chr10:27950886-27950887
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1168575	0.88[ASN][1000 genomes]
rs1168577	0.85[ASN][1000 genomes]
rs1168584	0.88[ASN][1000 genomes]
rs1168587	0.91[ASN][1000 genomes]
rs1168592	0.81[ASN][1000 genomes]
rs1177564	0.88[ASN][1000 genomes]
rs1494196	0.96[ASN][1000 genomes]
rs1494197	0.96[ASN][1000 genomes]
rs1494199	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1494200	0.88[EUR][1000 genomes]
rs1532315	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1552879	0.88[EUR][1000 genomes]
rs1603021	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1613987	0.83[ASN][1000 genomes]
rs1620830	0.93[ASN][1000 genomes]
rs1687721	0.98[ASN][1000 genomes]
rs1690682	0.96[ASN][1000 genomes]
rs2130809	0.86[JPT][hapmap]
rs2253230	0.86[JPT][hapmap]
rs2451923	0.82[ASN][1000 genomes]
rs2492907	0.96[ASN][1000 genomes]
rs2505135	0.82[ASN][1000 genomes]
rs2637282	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2637283	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2637300	0.88[EUR][1000 genomes]
rs2637309	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2637311	0.88[EUR][1000 genomes]
rs2637312	0.88[EUR][1000 genomes]
rs2637313	0.88[EUR][1000 genomes]
rs2637331	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2642275	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2642277	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2642280	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2642281	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2642283	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2642284	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2642285	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2642287	0.87[EUR][1000 genomes]
rs2642288	0.86[EUR][1000 genomes]
rs2642289	0.88[EUR][1000 genomes]
rs2642297	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642298	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642301	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2808262	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2808263	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2808264	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2808267	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2808269	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2808270	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2808271	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2808272	0.96[ASN][1000 genomes]
rs2808273	0.96[ASN][1000 genomes]
rs2808277	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2808278	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2815513	0.88[EUR][1000 genomes]
rs2815514	0.88[EUR][1000 genomes]
rs2815515	0.88[EUR][1000 genomes]
rs2815517	0.88[EUR][1000 genomes]
rs2815518	0.87[EUR][1000 genomes]
rs2815520	0.88[EUR][1000 genomes]
rs2815521	0.88[EUR][1000 genomes]
rs2815522	0.88[EUR][1000 genomes]
rs2815523	0.87[EUR][1000 genomes]
rs2815524	0.88[EUR][1000 genomes]
rs2815525	0.88[EUR][1000 genomes]
rs2815526	0.88[EUR][1000 genomes]
rs2815529	0.88[EUR][1000 genomes]
rs2815530	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2815531	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2815532	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2815533	0.90[EUR][1000 genomes]
rs2815535	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2815536	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2815537	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2815538	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2815540	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2815541	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2999979	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs997462	0.88[EUR][1000 genomes]
rs997750	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550241	chr10:27569521-28025771	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3368825	chr10:27864181-28043820	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv894985	chr10:27869503-27957785	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv894986	chr10:27904646-27957785	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27933800-27963600	Weak transcription	Ovary	ovary
2	chr10:27941600-27963600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:27947000-27951000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr10:27947200-27951400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr10:27948600-27951000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr10:27948600-27954200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr10:27948800-27951800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr10:27949200-27951000	Enhancers	Adipose Nuclei	Adipose
9	chr10:27949400-27951200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr10:27949600-27951200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:27950400-27951000	Enhancers	HSMM	muscle
12	chr10:27950400-27951000	Enhancers	HSMMtube	muscle
13	chr10:27950400-27953400	Enhancers	Hela-S3	cervix
14	chr10:27950600-27951000	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr10:27950800-27951000	Enhancers	NHDF-Ad	bronchial
16	chr10:27950800-27952600	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links