Variant report

Variant	rs10516154
Chromosome Location	chr5:59791348-59791349
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:59784827..59787759-chr5:59790470..59792339,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10045433	1.00[CHD][hapmap]
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	0.86[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];0.80[EUR][1000 genomes]
rs16878190	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
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]
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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10516154	NDUFAF2	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59782000-59801000	Weak transcription	Fetal Brain Male	brain
2	chr5:59784600-59791800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:59784600-59794200	Weak transcription	Gastric	stomach
4	chr5:59784800-59793600	Weak transcription	Colon Smooth Muscle	Colon
5	chr5:59785200-59791800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:59785200-59793400	Weak transcription	Fetal Stomach	stomach
7	chr5:59787200-59793400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:59788800-59791800	Enhancers	HepG2	liver
9	chr5:59788800-59792600	Enhancers	A549	lung
10	chr5:59789000-59791400	Enhancers	Primary B cells from cord blood	blood
11	chr5:59789400-59791400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:59789400-59791600	Enhancers	Primary B cells from peripheral blood	blood
13	chr5:59789400-59793800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:59789600-59791800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr5:59789600-59794000	Weak transcription	NHEK	skin
16	chr5:59789600-59795400	Weak transcription	Aorta	Aorta
17	chr5:59789800-59793600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:59790000-59792000	Enhancers	Brain Hippocampus Middle	brain
19	chr5:59790000-59795000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:59790200-59791400	Weak transcription	Osteobl	bone
21	chr5:59790200-59793400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr5:59790200-59794200	Enhancers	Brain Substantia Nigra	brain
23	chr5:59790400-59794800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:59790600-59792200	Enhancers	Brain Anterior Caudate	brain
25	chr5:59790600-59792600	Enhancers	GM12878-XiMat	blood
26	chr5:59790800-59792000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:59791000-59794800	Enhancers	Brain Cingulate Gyrus	brain
28	chr5:59791000-59795200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:59791200-59791800	Enhancers	Brain Angular Gyrus	brain
30	chr5:59791200-59791800	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr5:59791200-59792000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:59791200-59792200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:59791200-59795000	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links