Variant report

Variant	rs4681317
Chromosome Location	chr3:146077980-146077981
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1033116	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1033117	0.85[ASN][1000 genomes]
rs10935620	0.81[EUR][1000 genomes]
rs10935631	0.83[JPT][hapmap]
rs10935632	0.83[JPT][hapmap]
rs12485655	0.93[ASN][1000 genomes]
rs12487546	0.83[JPT][hapmap]
rs12494817	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495507	0.95[ASN][1000 genomes]
rs13068178	0.83[JPT][hapmap]
rs13088225	0.82[JPT][hapmap]
rs13089349	0.85[ASN][1000 genomes]
rs13090489	0.83[JPT][hapmap]
rs1403641	0.83[JPT][hapmap]
rs1403645	0.83[JPT][hapmap]
rs1512077	0.95[ASN][1000 genomes]
rs1523336	0.88[JPT][hapmap]
rs1606433	0.81[EUR][1000 genomes]
rs1608392	0.83[JPT][hapmap]
rs1858387	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1949150	0.80[EUR][1000 genomes]
rs2137227	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2137228	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2137229	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2203130	0.81[EUR][1000 genomes]
rs2867085	0.81[EUR][1000 genomes]
rs2867086	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2867087	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4234358	0.83[JPT][hapmap]
rs4355250	0.83[JPT][hapmap]
rs4553948	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4563382	0.85[ASN][1000 genomes]
rs4572737	0.83[JPT][hapmap]
rs4681119	0.83[JPT][hapmap]
rs4681315	0.81[EUR][1000 genomes]
rs56004717	0.84[ASN][1000 genomes]
rs6440428	0.86[ASN][1000 genomes]
rs6767156	0.83[JPT][hapmap]
rs6772169	0.81[ASN][1000 genomes]
rs7430021	0.82[EUR][1000 genomes]
rs7642687	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7645939	0.83[JPT][hapmap]
rs7653701	0.83[JPT][hapmap]
rs907491	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9842818	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[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	nsv998388	chr3:145960954-146087749	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv19457	chr3:146071361-146085768	Weak transcription ZNF genes & repeats Enhancers Active TSS	n/a	n/a	inside rSNPs	diseases
3	esv3428127	chr3:146073560-146082194	ZNF genes & repeats Enhancers Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases
4	esv3363313	chr3:146075716-146081641	Weak transcription Active TSS ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4681317	ZIC1	cis	cerebellum	SCAN
rs4681317	AADAC	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146077200-146079200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
2	chr3:146077200-146079400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:146077200-146081200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:146077400-146079000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell

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