Variant report

Variant	rs9547952
Chromosome Location	chr13:38138689-38138690
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRPC4-2	chr13:38138656-38139140	NONHSAT033251

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11840960	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12428760	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12585355	0.95[ASN][1000 genomes]
rs17056105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17056258	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1924293	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35092366	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41473348	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4943526	1.00[CEU][hapmap]
rs57400150	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59664730	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60396302	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6563562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7335337	1.00[JPT][hapmap]
rs73452525	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73452550	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73452553	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73452556	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997479	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9532083	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9532102	0.82[CEU][hapmap]
rs9547948	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9547949	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9547950	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9547955	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9547956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9547971	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9547972	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9547973	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9547975	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9547982	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9547984	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9547993	0.83[EUR][1000 genomes]
rs9547995	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9548009	0.82[CEU][hapmap]
rs9548024	0.82[CEU][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	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1038850	chr13:37820489-38209571	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv34109	chr13:37843819-38276391	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1045716	chr13:37952062-38394595	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv832583	chr13:38030752-38202000	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv818956	chr13:38131993-38153351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
7	esv3403702	chr13:38138002-38139000	Strong transcription Weak transcription	lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38133400-38154800	Weak transcription	Fetal Stomach	stomach
2	chr13:38134000-38149600	Weak transcription	Fetal Muscle Leg	muscle
3	chr13:38134000-38153800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr13:38134600-38143600	Weak transcription	Placenta	Placenta
5	chr13:38135200-38168800	Strong transcription	Osteobl	bone
6	chr13:38135600-38139200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr13:38135600-38165400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr13:38135800-38145600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr13:38137600-38141600	Weak transcription	NH-A	brain
10	chr13:38138000-38145600	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr13:38138600-38140800	Strong transcription	Fetal Lung	lung

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