Variant report

Variant	rs2869462
Chromosome Location	chr4:76934719-76934720
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10007919	0.94[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10009947	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10021434	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10029157	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10031733	0.84[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10031983	0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10518143	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374321	0.88[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12374370	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12649185	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13111494	0.94[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs13112512	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13118503	0.94[CEU][hapmap];0.86[CHB][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13129896	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13130917	0.89[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs1394916	1.00[YRI][hapmap]
rs17001247	0.88[CEU][hapmap];0.86[CHB][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1857821	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2242470	0.94[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271528	0.94[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276886	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28375800	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28422144	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28451731	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28532601	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28535831	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28588114	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28595360	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28647886	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34630680	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34740469	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3733238	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3796484	0.84[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4241577	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4429750	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4859567	0.88[CEU][hapmap]
rs4859570	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4859571	0.88[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4859572	0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4859573	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4859577	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859578	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859580	0.80[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859609	0.86[CHB][hapmap]
rs55876513	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66498356	0.83[ASN][1000 genomes]
rs6847815	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs884004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884304	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs9994667	0.94[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][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	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2869462	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs2869462	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs2869462	NAAA	cis	Muscle Skeletal	GTEx
rs2869462	NAAA	cis	Artery Aorta	GTEx
rs2869462	NAAA	cis	Whole Blood	GTEx
rs2869462	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs2869462	NAAA	cis	Esophagus Mucosa	GTEx
rs2869462	NAAA	cis	Esophagus Muscularis	GTEx
rs2869462	CXCL10	cis	multi-tissue	Pritchard
rs2869462	ENSG00000169245	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76932600-76935400	Enhancers	Liver	Liver
2	chr4:76933000-76937400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:76933000-76937600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:76933000-76937600	Weak transcription	Placenta	Placenta
5	chr4:76933000-76937600	Weak transcription	Pancreas	Pancrea
6	chr4:76933400-76935200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr4:76933400-76936000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr4:76933400-76936200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr4:76933400-76936200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:76933400-76937600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:76933600-76935000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:76933600-76936000	Weak transcription	Primary B cells from cord blood	blood
13	chr4:76933600-76937400	Weak transcription	Fetal Thymus	thymus
14	chr4:76933600-76937600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:76933800-76934800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr4:76933800-76935000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:76933800-76937600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr4:76934000-76935000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:76934000-76935800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:76934000-76936800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:76934000-76937200	Enhancers	GM12878-XiMat	blood
22	chr4:76934000-76938000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr4:76934200-76935000	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr4:76934200-76936000	Enhancers	Fetal Intestine Small	intestine
25	chr4:76934200-76936400	Enhancers	Fetal Intestine Large	intestine
26	chr4:76934400-76937400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr4:76934400-76937400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:76934400-76937400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:76934400-76937600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:76934400-76937600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:76934400-76944200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr4:76934600-76937400	Weak transcription	HMEC	breast
33	chr4:76934600-76937400	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links