Variant report

Variant	rs4679904
Chromosome Location	chr3:160340896-160340897
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10460866	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10923	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs10936203	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs10936210	0.82[EUR][1000 genomes]
rs11709232	0.84[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap]
rs11711627	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11712392	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713230	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719750	0.84[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap]
rs11721112	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11927913	0.82[EUR][1000 genomes]
rs12152435	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12630956	0.81[EUR][1000 genomes]
rs12638633	0.84[EUR][1000 genomes]
rs12639488	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13062928	0.82[ASN][1000 genomes]
rs13065269	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074231	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075424	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13085507	0.82[ASN][1000 genomes]
rs1403045	0.83[CEU][hapmap]
rs1522285	0.83[EUR][1000 genomes]
rs16831337	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs17236494	0.84[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap]
rs17826257	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1882125	0.81[CEU][hapmap];0.90[CHB][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1920650	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1920663	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1980277	0.83[EUR][1000 genomes]
rs2141668	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2178451	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35008770	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35498840	0.81[CEU][hapmap];0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs3732706	0.81[JPT][hapmap]
rs3851365	0.81[JPT][hapmap]
rs4133253	0.80[CEU][hapmap]
rs4679892	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4679903	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57718211	0.82[ASN][1000 genomes]
rs6803670	0.83[EUR][1000 genomes]
rs6806755	0.83[CEU][hapmap]
rs71314011	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73875285	0.83[EUR][1000 genomes]
rs73875290	0.84[EUR][1000 genomes]
rs7610939	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs7633839	0.81[CEU][hapmap]
rs7634255	0.81[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7644186	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	nsv877703	chr3:160325458-160398885	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Primary biliary cirrhosis	19458352	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4679904	IFT80	cis	cerebellum	SCAN
rs4679904	IFT80	cis	parietal	SCAN
rs4679904	RSRC1	cis	cerebellum	SCAN
rs4679904	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160338600-160342400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:160339400-160341200	Enhancers	Liver	Liver
3	chr3:160339600-160341200	Enhancers	Muscle Satellite Cultured Cells	--
4	chr3:160340200-160341000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:160340600-160341000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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