Variant report

Variant	rs4869277
Chromosome Location	chr5:95615651-95615652
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10045787	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10063744	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10065122	0.86[AFR][1000 genomes]
rs10515235	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10866767	0.82[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs11948972	0.86[MEX][hapmap]
rs11959068	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13153770	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13158163	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3811942	0.80[MEX][hapmap]
rs3922467	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4288139	0.90[AFR][1000 genomes]
rs4336380	0.90[AFR][1000 genomes]
rs4529218	0.82[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap]
rs4637573	0.82[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap]
rs4869278	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56376321	0.92[EUR][1000 genomes]
rs6556913	0.82[AFR][1000 genomes]
rs7444135	0.83[AMR][1000 genomes]
rs7710625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7730339	0.87[AMR][1000 genomes];0.93[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	nsv1030444	chr5:95353620-95995619	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv537810	chr5:95353620-95995619	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv830410	chr5:95505799-95666310	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4869277	FAM172A	cis	parietal	SCAN
rs4869277	ANKRD32	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95612600-95632400	Weak transcription	Aorta	Aorta
2	chr5:95613000-95623800	Weak transcription	HSMM	muscle
3	chr5:95613800-95616200	Enhancers	HepG2	liver
4	chr5:95614000-95615800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:95614200-95617200	Weak transcription	Esophagus	oesophagus
6	chr5:95614400-95617400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:95614800-95617400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:95614800-95617400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:95615000-95616400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:95615200-95616000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr5:95615200-95616000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:95615200-95616400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr5:95615400-95616400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:95615400-95616400	Flanking Active TSS	GM12878-XiMat	blood
15	chr5:95615400-95616400	Enhancers	HUVEC	blood vessel
16	chr5:95615400-95616400	Enhancers	Osteobl	bone
17	chr5:95615400-95616600	Enhancers	NH-A	brain
18	chr5:95615400-95617200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr5:95615600-95615800	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr5:95615600-95616000	Flanking Active TSS	HMEC	breast
21	chr5:95615600-95616000	Flanking Active TSS	NHEK	skin
22	chr5:95615600-95616200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:95615600-95616800	Enhancers	A549	lung
24	chr5:95615600-95617400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links