Variant report

Variant	rs1879684
Chromosome Location	chr4:142462518-142462519
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:142460579..142463426-chr4:142464667..142466425,2	MCF-7	breast:
2	chr4:142457149..142460025-chr4:142460806..142464017,3	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs12152590	0.95[EUR][1000 genomes]
rs12505744	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12508866	0.81[TSI][hapmap]
rs12513220	0.95[EUR][1000 genomes]
rs13106515	0.95[EUR][1000 genomes]
rs13111616	0.89[EUR][1000 genomes]
rs13120181	0.81[EUR][1000 genomes]
rs13122574	0.89[EUR][1000 genomes]
rs13127492	0.94[EUR][1000 genomes]
rs13132563	0.81[EUR][1000 genomes]
rs13133830	0.95[EUR][1000 genomes]
rs13142400	0.87[EUR][1000 genomes]
rs13145587	0.89[EUR][1000 genomes]
rs17362224	0.95[EUR][1000 genomes]
rs1949668	0.95[EUR][1000 genomes]
rs1949669	0.95[EUR][1000 genomes]
rs2049181	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2139992	0.95[EUR][1000 genomes]
rs34124780	0.95[EUR][1000 genomes]
rs34149126	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs34274316	0.95[EUR][1000 genomes]
rs34422514	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34579838	0.95[EUR][1000 genomes]
rs34865075	0.89[EUR][1000 genomes]
rs34899172	0.95[EUR][1000 genomes]
rs34962680	0.87[EUR][1000 genomes]
rs35308689	0.95[EUR][1000 genomes]
rs35372192	0.95[EUR][1000 genomes]
rs35720798	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35969143	0.95[EUR][1000 genomes]
rs36043894	0.83[EUR][1000 genomes]
rs36124988	0.94[EUR][1000 genomes]
rs4519867	0.82[EUR][1000 genomes]
rs4956301	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4956302	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57470227	0.80[ASN][1000 genomes]
rs62325330	0.88[EUR][1000 genomes]
rs62326618	0.95[EUR][1000 genomes]
rs62326619	0.95[EUR][1000 genomes]
rs62327371	0.89[EUR][1000 genomes]
rs62327372	0.89[EUR][1000 genomes]
rs62327373	0.80[EUR][1000 genomes]
rs62327375	0.89[EUR][1000 genomes]
rs62327376	0.89[EUR][1000 genomes]
rs62327381	0.85[EUR][1000 genomes]
rs67407219	0.95[EUR][1000 genomes]
rs6812199	0.83[EUR][1000 genomes]
rs6837400	0.89[EUR][1000 genomes]
rs6837886	0.81[EUR][1000 genomes]
rs72615929	0.80[ASN][1000 genomes]
rs72615930	0.80[ASN][1000 genomes]
rs72615931	0.80[ASN][1000 genomes]
rs72615932	0.80[ASN][1000 genomes]
rs72615934	0.80[ASN][1000 genomes]
rs72615935	0.80[ASN][1000 genomes]
rs72615936	0.80[ASN][1000 genomes]
rs72728300	0.95[EUR][1000 genomes]
rs72730041	0.81[EUR][1000 genomes]
rs7692755	0.83[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
rs1879684	TBC1D9	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142460200-142462600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr4:142461200-142464000	Enhancers	Osteobl	bone
3	chr4:142461800-142463800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr4:142461800-142463800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:142461800-142464400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:142462200-142463800	Enhancers	NHDF-Ad	bronchial
7	chr4:142462400-142463200	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links