Variant report

Variant	rs11840833
Chromosome Location	chr13:94378307-94378308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11838508	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11839972	0.81[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16949138	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16949141	0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16949153	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17468092	1.00[CEU][hapmap]
rs4144545	0.87[ASW][hapmap];0.86[GIH][hapmap]
rs4465475	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60455241	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6492674	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7323912	1.00[CEU][hapmap]
rs7331448	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs7335457	0.82[GIH][hapmap]
rs7985749	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7986313	0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9556321	0.88[ASW][hapmap];0.84[GIH][hapmap]
rs9589817	1.00[CEU][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948714	chr13:94100104-94699435	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv933807	chr13:94187158-94845505	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1039305	chr13:94229672-94398382	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1045230	chr13:94277683-94764671	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv562753	chr13:94283764-94402110	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv933758	chr13:94299302-94421378	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv916694	chr13:94360053-94423063	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs11840833	KLF4	trans	brain	seeQTL
rs11840833	OMD	trans	brain	seeQTL
rs11840833	FGL2	trans	brain	seeQTL
rs11840833	TNFRSF11B	trans	brain	seeQTL
rs11840833	SLPI	trans	brain	seeQTL
rs11840833	ANXA2	trans	brain	seeQTL
rs11840833	SLC26A2	trans	brain	seeQTL
rs11840833	OLFML2A	trans	brain	seeQTL
rs11840833	KLK1	trans	brain	seeQTL
rs11840833	SFRP2	trans	brain	seeQTL
rs11840833	UPK1B	trans	brain	seeQTL
rs11840833	CRABP1	trans	brain	seeQTL
rs11840833	ANXA1	trans	brain	seeQTL
rs11840833	SLC47A1	trans	brain	seeQTL
rs11840833	PTGDR	trans	brain	seeQTL
rs11840833	ENPP6	trans	brain	seeQTL
rs11840833	BMP5	trans	brain	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94376000-94378600	Weak transcription	Fetal Heart	heart
2	chr13:94376000-94379200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr13:94376000-94380000	Weak transcription	Liver	Liver
4	chr13:94376200-94379200	Weak transcription	Osteobl	bone
5	chr13:94377400-94378400	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr13:94377600-94379000	Enhancers	Colon Smooth Muscle	Colon
7	chr13:94377800-94380200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr13:94378000-94378400	Weak transcription	Ovary	ovary
9	chr13:94378000-94379200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr13:94378200-94378400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr13:94378200-94378600	Enhancers	Fetal Brain Male	brain
12	chr13:94378200-94378800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr13:94378200-94378800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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