Variant report

Variant	rs9968292
Chromosome Location	chr4:152297368-152297369
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10028035	0.85[AMR][1000 genomes]
rs10454251	0.83[AMR][1000 genomes]
rs11099811	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11099815	0.85[AMR][1000 genomes]
rs11099816	0.80[AMR][1000 genomes]
rs1143036	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11729923	0.83[AMR][1000 genomes]
rs11732407	0.91[GIH][hapmap]
rs11732918	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11733820	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11932398	0.83[AMR][1000 genomes]
rs12647555	0.89[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes]
rs1372976	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs1372977	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs1443087	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs1443088	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs1443089	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs1470280	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs1596290	0.82[AMR][1000 genomes]
rs2053566	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs2709812	0.83[AMR][1000 genomes]
rs2709813	0.85[AMR][1000 genomes]
rs2709815	0.83[AMR][1000 genomes]
rs2709816	0.82[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes]
rs2709817	0.83[AMR][1000 genomes]
rs2709818	0.83[AMR][1000 genomes]
rs2709819	0.83[AMR][1000 genomes]
rs2709820	0.82[AMR][1000 genomes]
rs2709821	0.83[AMR][1000 genomes]
rs2709822	0.84[AMR][1000 genomes]
rs2709823	0.84[AMR][1000 genomes]
rs2709825	0.83[AMR][1000 genomes]
rs2709826	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2709827	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2709828	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes]
rs2709829	0.85[AMR][1000 genomes]
rs2709831	0.89[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes]
rs2709832	0.84[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes]
rs2709833	0.80[AMR][1000 genomes]
rs2709834	0.84[AMR][1000 genomes]
rs2709838	0.83[AMR][1000 genomes]
rs2709842	0.83[AMR][1000 genomes]
rs2709844	0.83[AMR][1000 genomes]
rs2724547	0.83[AMR][1000 genomes]
rs2724550	0.83[AMR][1000 genomes]
rs2724551	0.85[AMR][1000 genomes]
rs2724555	0.85[AMR][1000 genomes]
rs2724558	0.82[AMR][1000 genomes]
rs2724563	0.83[AMR][1000 genomes]
rs2724564	0.83[AMR][1000 genomes]
rs2724565	0.84[AMR][1000 genomes]
rs2724567	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes]
rs2724568	0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes]
rs2724571	0.83[AMR][1000 genomes]
rs2724573	0.91[GIH][hapmap]
rs2724574	0.83[AMR][1000 genomes]
rs2724577	0.89[CHB][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes]
rs2724578	0.83[AMR][1000 genomes]
rs2724580	0.83[AMR][1000 genomes]
rs28549769	0.82[AMR][1000 genomes]
rs28622593	0.83[AMR][1000 genomes]
rs28666858	0.81[AMR][1000 genomes]
rs4235219	0.85[AMR][1000 genomes]
rs4254751	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4263379	0.89[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes]
rs4266275	0.85[AMR][1000 genomes]
rs4473638	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4519779	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696088	0.83[AMR][1000 genomes]
rs4696089	0.83[AMR][1000 genomes]
rs4696092	0.83[AMR][1000 genomes]
rs4696256	0.80[EUR][1000 genomes]
rs4696259	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696260	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696261	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57585665	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59714108	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62327196	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6813735	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6843639	0.81[AMR][1000 genomes]
rs6845648	0.83[AMR][1000 genomes]
rs6851814	0.81[AMR][1000 genomes]
rs7657670	0.85[AMR][1000 genomes]
rs7657747	0.83[AMR][1000 genomes]
rs7658169	0.85[AMR][1000 genomes]
rs7676059	0.83[AMR][1000 genomes]
rs7676922	0.83[AMR][1000 genomes]
rs7677131	0.85[AMR][1000 genomes]
rs7678823	0.85[AMR][1000 genomes]
rs7680013	0.83[AMR][1000 genomes]
rs7680236	0.83[AMR][1000 genomes]
rs7682770	0.83[AMR][1000 genomes]
rs7684462	0.85[AMR][1000 genomes]
rs7691601	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7698816	0.85[AMR][1000 genomes]
rs9994482	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1025192	chr4:152202627-152498890	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537307	chr4:152202627-152498890	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv880624	chr4:152280646-152549112	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats 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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9968292	FAM160A1	cis	cerebellum	SCAN
rs9968292	PET112L	cis	parietal	SCAN
rs9968292	FGG	cis	parietal	SCAN
rs9968292	FAM160A1	cis	parietal	SCAN
rs9968292	PLRG1	cis	cerebellum	SCAN
rs9968292	FAM160A1	cis	Whole Blood	GTEx
rs9968292	SH3D19	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152293800-152298200	Weak transcription	HepG2	liver
2	chr4:152294200-152297400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:152297200-152297400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:152297200-152297800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr4:152297200-152298200	Enhancers	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links