Variant report

Variant	rs4923405
Chromosome Location	chr11:26927697-26927698
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10835084	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11029745	0.91[ASN][1000 genomes]
rs12275216	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12275357	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12279670	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12280480	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12282988	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12287918	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12288441	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12574167	0.94[ASN][1000 genomes]
rs12574501	0.94[ASN][1000 genomes]
rs12574926	0.81[EUR][1000 genomes]
rs12577148	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1450220	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1450221	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16916312	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1822893	0.84[ASN][1000 genomes]
rs1822894	0.84[ASN][1000 genomes]
rs1901076	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2350932	0.81[ASN][1000 genomes]
rs2350934	0.83[JPT][hapmap]
rs4329641	0.81[ASN][1000 genomes]
rs4922777	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4923400	0.81[ASN][1000 genomes]
rs4923408	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56361643	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58646119	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58789402	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58878618	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59761353	0.80[EUR][1000 genomes]
rs60690634	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61888261	0.97[ASN][1000 genomes]
rs6484255	0.88[ASN][1000 genomes]
rs7101730	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7105515	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7108314	0.83[JPT][hapmap]
rs7111033	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9666797	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv1044544	chr11:26506962-26967285	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv916187	chr11:26576875-27328603	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv897146	chr11:26913936-27019331	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv983219	chr11:26926565-26932064	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4923405	SLC5A12	cis	cerebellum	SCAN
rs4923405	METT5D1	cis	cerebellum	SCAN
rs4923405	FSHB	cis	parietal	SCAN
rs4923405	ANO3	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:26925200-26928000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr11:26926000-26936400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:26926400-26931600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr11:26927000-26931800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr11:26927200-26930200	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:26927200-26931800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr11:26927200-26932200	Weak transcription	Fetal Lung	lung
8	chr11:26927200-26936200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:26927400-26931800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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