Variant report

Variant	rs875426
Chromosome Location	chr18:29143098-29143099
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];0.82[EUR][1000 genomes]
rs1551001	0.82[EUR][1000 genomes]
rs1551002	0.97[EUR][1000 genomes]
rs1551003	0.85[CEU][hapmap]
rs1667225	0.94[EUR][1000 genomes]
rs1667229	0.98[EUR][1000 genomes]
rs1667230	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1667234	0.95[EUR][1000 genomes]
rs1667235	0.95[EUR][1000 genomes]
rs1791208	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1791209	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1791212	0.98[EUR][1000 genomes]
rs1791215	0.82[EUR][1000 genomes]
rs1791218	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs1941931	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4315413	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4799575	0.80[EUR][1000 genomes]
rs875425	0.98[EUR][1000 genomes]
rs877597	0.82[EUR][1000 genomes]
rs9304102	0.85[CEU][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs9951041	0.87[ASN][1000 genomes]
rs9963742	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9963820	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9963959	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[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	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
rs875426	B4GALT6	cis	cerebellum	SCAN
rs875426	SGPP2	trans	cerebellum	SCAN
rs875426	DSC1	cis	parietal	SCAN

Chromatin state (count:9 , 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	chr18:29142200-29143800	Enhancers	HepG2	liver
4	chr18:29142600-29143200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr18:29142600-29143600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr18:29142600-29145600	Enhancers	Liver	Liver
7	chr18:29142800-29143200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr18:29143000-29143200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr18:29143000-29144200	Weak transcription	Fetal Intestine Large	intestine

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