Variant report

Variant	rs6138396
Chromosome Location	chr20:24852333-24852334
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1007881	0.86[JPT][hapmap]
rs1029033	0.88[AFR][1000 genomes]
rs1056036	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11087486	0.83[ASN][1000 genomes]
rs11700073	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11905625	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12625319	0.80[ASN][1000 genomes]
rs1535042	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1888655	0.86[AFR][1000 genomes]
rs2008275	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2179732	1.00[JPT][hapmap]
rs2235847	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs227625	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs227633	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs227634	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs227650	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs227653	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs35326290	0.86[AFR][1000 genomes]
rs3746330	1.00[JPT][hapmap]
rs4594518	0.87[ASN][1000 genomes]
rs4815351	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4815357	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6036943	0.93[AFR][1000 genomes]
rs6050051	0.93[AFR][1000 genomes]
rs6050118	0.87[ASN][1000 genomes]
rs6050198	1.00[CHB][hapmap]
rs6050201	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6050249	1.00[JPT][hapmap]
rs6050255	0.86[JPT][hapmap]
rs6050259	0.86[JPT][hapmap]
rs6050261	0.86[JPT][hapmap]
rs6083628	0.82[AFR][1000 genomes]
rs6083652	0.89[AFR][1000 genomes]
rs6083699	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6083709	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6106968	0.88[AFR][1000 genomes]
rs6114980	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6114981	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6114984	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6132775	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6132777	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6132778	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6132784	1.00[JPT][hapmap]
rs6132789	0.86[JPT][hapmap]
rs6138406	0.87[ASN][1000 genomes]
rs6138437	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6138442	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6138453	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6138455	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6138457	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6138458	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6138466	1.00[JPT][hapmap]
rs6138473	0.86[JPT][hapmap]
rs6138474	0.86[JPT][hapmap]
rs6138475	0.86[JPT][hapmap]
rs6515538	0.87[AFR][1000 genomes]
rs6707	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7268095	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs8125909	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs8183891	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061412	chr20:24629468-24887869	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv544216	chr20:24629468-24887869	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1061455	chr20:24733120-24861801	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544218	chr20:24733120-24861801	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers 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	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 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	chr20:24851200-24853200	Enhancers	Brain Hippocampus Middle	brain
2	chr20:24851400-24852400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:24851400-24852400	Enhancers	Spleen	Spleen
4	chr20:24851400-24853200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr20:24851400-24854200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr20:24851400-24854200	Enhancers	GM12878-XiMat	blood
7	chr20:24851600-24852400	Enhancers	Brain Cingulate Gyrus	brain
8	chr20:24851600-24853200	Enhancers	Fetal Brain Male	brain
9	chr20:24851600-24853200	Enhancers	Fetal Lung	lung
10	chr20:24851800-24853000	Enhancers	Brain Angular Gyrus	brain
11	chr20:24851800-24853000	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr20:24851800-24853000	Weak transcription	Esophagus	oesophagus
13	chr20:24851800-24854000	Enhancers	Fetal Thymus	thymus
14	chr20:24852000-24853000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr20:24852200-24852600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr20:24852200-24852800	Bivalent Enhancer	Fetal Stomach	stomach

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