Variant report

Variant	rs16878190
Chromosome Location	chr5:59804188-59804189
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10045433	1.00[CHD][hapmap]
rs10516154	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10939842	1.00[CHD][hapmap]
rs11746901	0.93[CEU][hapmap];1.00[CHD][hapmap]
rs11948687	0.93[CEU][hapmap]
rs11957512	1.00[ASN][1000 genomes]
rs11960912	1.00[ASN][1000 genomes]
rs12153271	1.00[CHD][hapmap]
rs12153798	0.87[CEU][hapmap]
rs12188950	0.93[CEU][hapmap];1.00[CHD][hapmap]
rs16877912	1.00[CHD][hapmap]
rs16878144	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap]
rs16878304	1.00[ASN][1000 genomes]
rs2061252	1.00[ASN][1000 genomes]
rs2061254	1.00[ASN][1000 genomes]
rs2409763	1.00[ASN][1000 genomes]
rs2441051	1.00[ASN][1000 genomes]
rs2441052	1.00[ASN][1000 genomes]
rs2591635	1.00[ASN][1000 genomes]
rs2606688	1.00[ASN][1000 genomes]
rs286150	1.00[ASN][1000 genomes]
rs286151	1.00[ASN][1000 genomes]
rs286152	1.00[ASN][1000 genomes]
rs286157	1.00[ASN][1000 genomes]
rs286159	1.00[ASN][1000 genomes]
rs2898278	0.82[CEU][hapmap]
rs3857237	1.00[ASN][1000 genomes]
rs3887175	1.00[ASN][1000 genomes]
rs3909458	1.00[ASN][1000 genomes]
rs6449470	1.00[CHD][hapmap]
rs6872509	1.00[ASN][1000 genomes]
rs7719095	0.93[CEU][hapmap]
rs7728865	1.00[ASN][1000 genomes]
rs9686946	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv598297	chr5:59734004-59862453	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59794800-59805800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr5:59801000-59804400	Enhancers	Fetal Brain Male	brain
3	chr5:59801400-59813800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:59801800-59805400	Weak transcription	Fetal Muscle Leg	muscle
5	chr5:59801800-59813000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:59802000-59805800	Weak transcription	Brain Hippocampus Middle	brain
7	chr5:59802000-59806800	Enhancers	GM12878-XiMat	blood
8	chr5:59802200-59805200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:59802200-59805600	Weak transcription	Brain Substantia Nigra	brain
10	chr5:59802200-59806000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr5:59802400-59812400	Weak transcription	Primary B cells from cord blood	blood
12	chr5:59803400-59804200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr5:59803400-59804400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:59803600-59807200	Enhancers	Rectal Smooth Muscle	rectum
15	chr5:59803800-59804200	Enhancers	Placenta Amnion	Placenta Amnion
16	chr5:59803800-59804200	Enhancers	Osteobl	bone
17	chr5:59803800-59804800	Enhancers	Colon Smooth Muscle	Colon
18	chr5:59803800-59805800	Weak transcription	Fetal Stomach	stomach

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