Variant report

Variant	rs11209002
Chromosome Location	chr1:67590461-67590462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10732838	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10749772	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10889656	0.94[CEU][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11208997	0.90[TSI][hapmap]
rs11209000	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11806560	1.00[CHB][hapmap]
rs17129650	1.00[CHB][hapmap]
rs1885276	0.86[TSI][hapmap]
rs1885279	1.00[CHB][hapmap]
rs1885280	1.00[CHB][hapmap]
rs2863202	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3762320	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4655520	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6588240	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6687611	0.80[CEU][hapmap];0.90[TSI][hapmap]
rs6701962	0.90[TSI][hapmap]
rs7517744	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7528804	0.86[TSI][hapmap]
rs7531589	0.90[TSI][hapmap]
rs7535494	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]

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	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
5	nsv870950	chr1:67575549-67627260	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Crohn's disease	17804789	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11209002	SLC35D1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67585400-67600400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:67589000-67591400	Weak transcription	NHEK	skin
3	chr1:67589800-67590600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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