Variant report

Variant	rs41142
Chromosome Location	chr5:111340370-111340371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10059738	0.85[ASN][1000 genomes]
rs10063079	0.84[ASN][1000 genomes]
rs10463623	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10463624	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs11241146	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1493453	0.91[ASN][1000 genomes]
rs1494585	0.90[ASN][1000 genomes]
rs1507844	0.88[CEU][hapmap]
rs1540687	0.87[CEU][hapmap]
rs168875	0.82[ASN][1000 genomes]
rs2047070	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2048155	0.86[CHB][hapmap];0.90[ASN][1000 genomes]
rs255910	0.88[ASN][1000 genomes]
rs255916	0.82[ASN][1000 genomes]
rs255920	0.81[ASN][1000 genomes]
rs255928	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs255929	0.96[ASN][1000 genomes]
rs255930	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs25790	0.87[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs26539	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs26540	0.96[ASN][1000 genomes]
rs26541	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs26542	0.97[ASN][1000 genomes]
rs26543	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs26545	0.90[ASN][1000 genomes]
rs26546	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs26557	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs26558	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs26559	0.98[ASN][1000 genomes]
rs26560	0.99[ASN][1000 genomes]
rs26561	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26562	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26563	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27535	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34924	0.96[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs34928	0.90[ASN][1000 genomes]
rs34930	0.90[ASN][1000 genomes]
rs34931	0.90[ASN][1000 genomes]
rs34941	0.95[ASN][1000 genomes]
rs34942	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35303575	0.91[ASN][1000 genomes]
rs35658682	0.90[ASN][1000 genomes]
rs36061964	0.86[ASN][1000 genomes]
rs36069145	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36133922	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs42308	0.90[ASN][1000 genomes]
rs466033	0.95[CEU][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs474807	0.84[ASN][1000 genomes]
rs490821	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs490983	0.87[ASN][1000 genomes]
rs504582	0.85[ASN][1000 genomes]
rs508089	0.87[ASN][1000 genomes]
rs560063	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs593236	0.86[ASN][1000 genomes]
rs624694	0.96[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs6881837	0.86[ASN][1000 genomes]
rs6882073	0.84[ASN][1000 genomes]
rs6882205	0.86[ASN][1000 genomes]
rs712660	0.87[ASN][1000 genomes]
rs7710690	0.95[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs7730997	0.88[ASN][1000 genomes]
rs7735316	0.87[ASN][1000 genomes]
rs9326846	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs980888	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599367	chr5:110924280-111602713	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111334800-111341000	Weak transcription	Psoas Muscle	Psoas
2	chr5:111337200-111342600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:111338000-111343000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:111339600-111343600	Enhancers	Osteobl	bone
5	chr5:111339800-111341600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:111339800-111343200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:111339800-111343200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:111340000-111340800	Enhancers	Thymus	Thymus
9	chr5:111340000-111341200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:111340000-111341400	Enhancers	GM12878-XiMat	blood
11	chr5:111340000-111341600	Enhancers	HMEC	breast
12	chr5:111340000-111341600	Enhancers	HSMM	muscle
13	chr5:111340000-111342800	Enhancers	NHLF	lung
14	chr5:111340000-111343000	Enhancers	Muscle Satellite Cultured Cells	--
15	chr5:111340200-111341000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:111340200-111341000	Flanking Active TSS	NHDF-Ad	bronchial
17	chr5:111340200-111341400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:111340200-111341400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:111340200-111341400	Enhancers	HSMMtube	muscle
20	chr5:111340200-111341600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:111340200-111341600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:111340200-111341600	Enhancers	NHEK	skin
23	chr5:111340200-111343200	Enhancers	NH-A	brain

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