Variant report

Variant	rs2171363
Chromosome Location	chr12:72360264-72360265
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10748188	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784946	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10784947	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10879345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10879346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10879349	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10879350	0.87[JPT][hapmap]
rs10879351	0.92[CEU][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap]
rs11179002	1.00[JPT][hapmap]
rs11179014	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11179027	0.86[JPT][hapmap]
rs11179033	0.87[JPT][hapmap]
rs11179039	0.92[CEU][hapmap];0.81[GIH][hapmap]
rs11834097	0.87[JPT][hapmap]
rs11834114	0.87[JPT][hapmap]
rs12229394	0.87[JPT][hapmap]
rs12319219	0.86[JPT][hapmap]
rs12322900	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1352250	0.92[CEU][hapmap]
rs1386498	0.90[CEU][hapmap]
rs1532008	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs1843811	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2171365	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2368049	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs34708908	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4362186	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4531512	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4641528	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4760750	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4760754	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs4760755	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs4760815	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57986383	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6582073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6582074	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6582077	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6582078	0.91[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6582079	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6582080	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7305115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7309686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7487961	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7954105	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7954142	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7955501	0.92[CEU][hapmap]
rs7963720	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7967686	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7969114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7978692	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7979770	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048478	chr12:72145703-72401712	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv541530	chr12:72145703-72401712	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv518498	chr12:72307616-72508779	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1054578	chr12:72307616-72509341	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	esv1847884	chr12:72356955-72360264	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2171363	SEPT14	trans	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:72353400-72362400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:72359600-72361800	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr12:72359800-72361000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr12:72359800-72361200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr12:72360000-72361000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:72360200-72360600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr12:72360200-72360800	Enhancers	H1 Cell Line	embryonic stem cell
8	chr12:72360200-72361200	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr12:72360200-72361400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:72360200-72361400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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