Variant report

Variant	rs6683455
Chromosome Location	chr1:67631706-67631707
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	RCOR1	chr1:67631705-67632298	GM12878	blood:	n/a	n/a
2	NFIC	chr1:67631695-67632339	GM12878	blood:	n/a	chr1:67632291-67632319
3	NFIC	chr1:67631079-67632458	GM12878	blood:	n/a	chr1:67632291-67632319
4	MEF2A	chr1:67631668-67632170	GM12878	blood:	n/a	n/a
5	FOXM1	chr1:67631700-67632355	GM12878	blood:	n/a	n/a
6	FOXM1	chr1:67631701-67632330	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
IL23R	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10127763	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap]
rs10889665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889668	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11801083	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1321156	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs1358748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358749	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884443	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2064691	0.94[EUR][1000 genomes]
rs2180296	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2863203	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4655521	0.91[EUR][1000 genomes]
rs4655522	0.90[EUR][1000 genomes]
rs4655681	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4655688	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6588247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs6666144	0.94[EUR][1000 genomes]
rs6684024	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687620	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703475	0.94[EUR][1000 genomes]
rs7518757	0.89[EUR][1000 genomes]
rs7540900	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461751	chr1:67479598-67689036	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv546445	chr1:67479598-67689036	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv461762	chr1:67551209-67648460	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv546446	chr1:67551209-67648460	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6683455	IL23R	cis	parietal	SCAN
rs6683455	WLS	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67628600-67635200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:67628800-67635000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr1:67628800-67635600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:67629400-67632000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:67630800-67632200	Enhancers	GM12878-XiMat	blood
6	chr1:67631400-67633400	Enhancers	Fetal Heart	heart
7	chr1:67631400-67637800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr1:67631600-67632200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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