Variant report

Variant	rs1667229
Chromosome Location	chr18:29142206-29142207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10468828	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs1551001	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1551002	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1551003	0.85[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1551004	0.81[EUR][1000 genomes]
rs1667225	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1667230	0.99[EUR][1000 genomes]
rs1667234	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1667235	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1791208	0.99[EUR][1000 genomes]
rs1791209	0.99[EUR][1000 genomes]
rs1791212	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1791215	0.83[EUR][1000 genomes]
rs1791218	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1941931	0.96[EUR][1000 genomes]
rs4315413	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4799575	0.81[EUR][1000 genomes]
rs875425	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs875426	0.98[EUR][1000 genomes]
rs877597	0.83[EUR][1000 genomes]
rs9304102	0.85[CEU][hapmap]
rs9963742	0.96[EUR][1000 genomes]
rs9963820	1.00[CEU][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes]
rs9963959	0.96[EUR][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	nsv1066692	chr18:28856066-29190505	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543674	chr18:28856066-29190505	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv916545	chr18:28898800-29166364	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833615	chr18:29008396-29192976	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv576635	chr18:29129931-29148814	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1667229	SGPP2	trans	cerebellum	SCAN
rs1667229	B4GALT6	cis	cerebellum	SCAN
rs1667229	DSC1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29129200-29143200	Weak transcription	Gastric	stomach
2	chr18:29136600-29145400	Weak transcription	Fetal Intestine Small	intestine
3	chr18:29139000-29142600	Weak transcription	Liver	Liver
4	chr18:29142200-29142800	Enhancers	Fetal Kidney	kidney
5	chr18:29142200-29142800	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr18:29142200-29143000	Enhancers	Fetal Intestine Large	intestine
7	chr18:29142200-29143800	Enhancers	HepG2	liver

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