Variant report

Variant	rs4672069
Chromosome Location	chr2:55987857-55987858
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11125600	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11676678	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11684982	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11693187	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11694759	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694790	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11887339	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614845	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13404193	0.84[ASN][1000 genomes]
rs1367228	1.00[CHB][hapmap]
rs1430191	1.00[CHB][hapmap];0.83[MEX][hapmap]
rs1430198	0.84[ASN][1000 genomes]
rs1430199	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1430200	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1465624	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1465625	0.90[ASN][1000 genomes]
rs1961386	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3791676	1.00[CHB][hapmap]
rs4233963	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671259	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6714513	1.00[CHB][hapmap]
rs6723918	0.84[ASN][1000 genomes]
rs6753814	1.00[CHB][hapmap]
rs6757057	1.00[CHB][hapmap]
rs6761334	0.89[ASN][1000 genomes]
rs7426380	1.00[CHB][hapmap]
rs7560508	0.84[ASN][1000 genomes]
rs7577894	0.89[ASN][1000 genomes]
rs9309269	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9309270	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs934274	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs934275	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs934276	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs934277	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[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	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv999962	chr2:55976574-56011517	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv997683	chr2:55976574-56013875	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4672069	CCDC85A	cis	parietal	SCAN
rs4672069	PEX26	trans	lymphoblastoid	seeQTL
rs4672069	EFEMP1	cis	parietal	SCAN
rs4672069	SCN10A	trans	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55985400-55991200	Enhancers	HMEC	breast
2	chr2:55986200-55989600	Enhancers	NHEK	skin
3	chr2:55986400-55989600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:55986600-55988600	Weak transcription	Aorta	Aorta
5	chr2:55986600-55990000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:55986800-55988000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:55986800-55988800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr2:55987200-55988200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:55987200-55988200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:55987400-55991400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr2:55987800-55988400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:55987800-55988600	Enhancers	HSMMtube	muscle
13	chr2:55987800-55989400	Enhancers	Adipose Nuclei	Adipose
14	chr2:55987800-55990200	Enhancers	HSMM	muscle

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