Variant report

Variant	rs4956301
Chromosome Location	chr4:142460479-142460480
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs12152590	0.86[EUR][1000 genomes]
rs12505744	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12508590	0.80[EUR][1000 genomes]
rs12509285	0.80[EUR][1000 genomes]
rs12511983	0.80[EUR][1000 genomes]
rs12513220	0.86[EUR][1000 genomes]
rs13106515	0.85[EUR][1000 genomes]
rs13111616	0.80[EUR][1000 genomes]
rs13113365	0.81[EUR][1000 genomes]
rs13117984	0.81[EUR][1000 genomes]
rs13119177	0.80[EUR][1000 genomes]
rs13122574	0.80[EUR][1000 genomes]
rs13127492	0.84[EUR][1000 genomes]
rs13133795	0.84[EUR][1000 genomes]
rs13133830	0.86[EUR][1000 genomes]
rs13145587	0.80[EUR][1000 genomes]
rs1357158	0.81[EUR][1000 genomes]
rs1402811	0.81[EUR][1000 genomes]
rs1402812	0.81[EUR][1000 genomes]
rs1521765	0.82[EUR][1000 genomes]
rs1521766	0.81[EUR][1000 genomes]
rs1581387	0.80[EUR][1000 genomes]
rs1581388	0.81[EUR][1000 genomes]
rs1581390	0.81[EUR][1000 genomes]
rs1608019	0.80[EUR][1000 genomes]
rs17362224	0.86[EUR][1000 genomes]
rs1879684	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1949667	0.82[EUR][1000 genomes]
rs1949668	0.86[EUR][1000 genomes]
rs1949669	0.86[EUR][1000 genomes]
rs2049181	0.87[EUR][1000 genomes]
rs2139992	0.86[EUR][1000 genomes]
rs34124780	0.86[EUR][1000 genomes]
rs34132448	0.81[EUR][1000 genomes]
rs34147541	0.81[EUR][1000 genomes]
rs34149126	0.87[EUR][1000 genomes]
rs34274316	0.86[EUR][1000 genomes]
rs34422514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34579838	0.85[EUR][1000 genomes]
rs34761999	0.80[EUR][1000 genomes]
rs34865075	0.80[EUR][1000 genomes]
rs34899172	0.86[EUR][1000 genomes]
rs35114853	0.81[EUR][1000 genomes]
rs35308689	0.86[EUR][1000 genomes]
rs35372192	0.86[EUR][1000 genomes]
rs35486128	0.80[EUR][1000 genomes]
rs35720798	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35881750	0.81[EUR][1000 genomes]
rs35969143	0.86[EUR][1000 genomes]
rs36124988	0.84[EUR][1000 genomes]
rs4956297	0.81[EUR][1000 genomes]
rs4956302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4956389	0.81[EUR][1000 genomes]
rs4956396	0.81[EUR][1000 genomes]
rs4956399	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs55912825	0.80[EUR][1000 genomes]
rs56051122	0.80[EUR][1000 genomes]
rs62326572	0.81[EUR][1000 genomes]
rs62326617	0.82[EUR][1000 genomes]
rs62326618	0.85[EUR][1000 genomes]
rs62326619	0.86[EUR][1000 genomes]
rs62327371	0.80[EUR][1000 genomes]
rs62327372	0.80[EUR][1000 genomes]
rs62327375	0.80[EUR][1000 genomes]
rs62327376	0.80[EUR][1000 genomes]
rs67407219	0.85[EUR][1000 genomes]
rs6810477	0.82[EUR][1000 genomes]
rs6812950	0.81[EUR][1000 genomes]
rs6826356	0.81[EUR][1000 genomes]
rs6837400	0.80[EUR][1000 genomes]
rs6858423	0.81[EUR][1000 genomes]
rs72728300	0.86[EUR][1000 genomes]
rs7677830	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880172	chr4:142355535-142565089	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv880173	chr4:142355535-142666106	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830094	chr4:142411738-142567788	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3401979	chr4:142434442-142803321	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv526989	chr4:142444108-142501053	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1018949	chr4:142451823-142732365	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4956301	TBC1D9	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142447200-142461200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:142460200-142462600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:142460400-142461800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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