Variant report

Variant	rs13096142
Chromosome Location	chr3:46281744-46281745
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr3:46281369-46281807	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
CCR3	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10865940	0.84[EUR][1000 genomes]
rs11130089	0.84[EUR][1000 genomes]
rs11711054	0.85[EUR][1000 genomes]
rs11923720	0.81[EUR][1000 genomes]
rs13081845	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13084656	1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1388604	0.90[JPT][hapmap]
rs1979672	0.81[MEX][hapmap]
rs2157057	0.84[EUR][1000 genomes]
rs2157059	0.80[EUR][1000 genomes]
rs2213291	0.84[EUR][1000 genomes]
rs2213292	0.84[EUR][1000 genomes]
rs34148191	0.84[EUR][1000 genomes]
rs34193387	0.84[EUR][1000 genomes]
rs34505903	0.84[EUR][1000 genomes]
rs35053103	0.84[EUR][1000 genomes]
rs35465430	0.83[EUR][1000 genomes]
rs35675823	0.84[EUR][1000 genomes]
rs35971655	0.84[EUR][1000 genomes]
rs36030342	0.84[EUR][1000 genomes]
rs41418050	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs41502550	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4683198	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62244827	0.84[EUR][1000 genomes]
rs62244840	0.84[EUR][1000 genomes]
rs62244848	0.83[EUR][1000 genomes]
rs6441950	0.90[JPT][hapmap]
rs6441953	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6441961	0.84[EUR][1000 genomes]
rs6441962	0.84[EUR][1000 genomes]
rs6441963	0.85[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs6441964	0.82[EUR][1000 genomes]
rs6767895	0.84[EUR][1000 genomes]
rs6771900	0.84[EUR][1000 genomes]
rs6775208	0.84[EUR][1000 genomes]
rs6788723	0.84[EUR][1000 genomes]
rs6793850	1.00[ASN][1000 genomes]
rs6794300	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6802288	0.87[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71327045	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs71615444	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7371987	0.90[JPT][hapmap];0.86[MEX][hapmap]
rs7372094	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7374654	0.85[EUR][1000 genomes]
rs7374671	0.90[EUR][1000 genomes]
rs7626249	0.84[EUR][1000 genomes]
rs7634816	0.84[EUR][1000 genomes]
rs963045	0.84[EUR][1000 genomes]
rs9813756	0.83[EUR][1000 genomes]
rs9818053	0.84[EUR][1000 genomes]
rs9842716	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9852052	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9853223	1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9856098	0.84[EUR][1000 genomes]
rs9875668	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Celiac disease	24999842	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13096142	KLHL18	cis	parietal	SCAN
rs13096142	RBM5	cis	parietal	SCAN
rs13096142	CCR5	trans	multi-tissue	Pritchard

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46278400-46282600	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr3:46278400-46283600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:46278600-46281800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:46278600-46282200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:46278600-46282800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr3:46278600-46283400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:46278600-46283400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:46281000-46281800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr3:46281000-46282000	Enhancers	H1 Cell Line	embryonic stem cell
10	chr3:46281200-46282000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:46281200-46282400	Enhancers	Fetal Heart	heart
12	chr3:46281400-46282200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:46281600-46282000	Enhancers	Fetal Thymus	thymus
14	chr3:46281600-46282600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:46281600-46285600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:46281600-46288600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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