Variant report

Variant	rs10028823
Chromosome Location	chr4:119098228-119098229
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10002349	1.00[AMR][1000 genomes]
rs10003652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10005659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10007553	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10018706	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10024548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10025029	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10025515	1.00[AMR][1000 genomes]
rs10030057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10031402	1.00[AMR][1000 genomes]
rs11931409	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11946772	1.00[AFR][1000 genomes]
rs13434557	1.00[AMR][1000 genomes]
rs28421577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28451256	1.00[AMR][1000 genomes]
rs28484271	1.00[AMR][1000 genomes]
rs28558085	1.00[AMR][1000 genomes]
rs28567841	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28576396	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28582030	1.00[AMR][1000 genomes]
rs28585079	1.00[AMR][1000 genomes]
rs28610040	1.00[AMR][1000 genomes]
rs28619162	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28634343	1.00[AMR][1000 genomes]
rs28665169	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28667620	1.00[AMR][1000 genomes]
rs28669076	1.00[AMR][1000 genomes]
rs28682376	1.00[AMR][1000 genomes]
rs28706008	1.00[AMR][1000 genomes]
rs28715892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28735538	1.00[AMR][1000 genomes]
rs28740899	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28771156	1.00[AMR][1000 genomes]
rs28776305	1.00[AMR][1000 genomes]
rs28823876	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28847597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28886020	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57461354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9307456	1.00[AMR][1000 genomes]
rs9994181	1.00[AMR][1000 genomes]

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	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1009076	chr4:118949490-119269424	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1001236	chr4:118949490-119271243	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv1008236	chr4:118989467-119154024	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv999152	chr4:119001143-119138322	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv34038	chr4:119035124-119455391	Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1001138	chr4:119095147-119461837	Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv537230	chr4:119095147-119461837	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10028823	MTHFSD	trans	lymphoblastoid	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119094000-119098400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:119094600-119101800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:119096200-119102000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr4:119096400-119098400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:119096400-119101800	Weak transcription	NHDF-Ad	bronchial
6	chr4:119096800-119102000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:119097200-119101800	Weak transcription	HMEC	breast
8	chr4:119097800-119098400	Enhancers	Dnd41	blood
9	chr4:119097800-119098800	Enhancers	NHLF	lung
10	chr4:119098000-119099200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:119098200-119099000	Enhancers	Osteobl	bone

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