Variant report

Variant	rs1490271
Chromosome Location	chr3:67345223-67345224
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1032319	0.92[ASN][1000 genomes]
rs1387872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1490253	0.82[ASN][1000 genomes]
rs1490255	0.82[ASN][1000 genomes]
rs1490256	0.82[ASN][1000 genomes]
rs1490262	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1586669	0.83[ASN][1000 genomes]
rs1586670	0.83[ASN][1000 genomes]
rs2054952	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2054953	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2054954	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2054955	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2054956	0.85[CHD][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2130543	0.83[ASN][1000 genomes]
rs2363664	0.83[ASN][1000 genomes]
rs2363707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2363708	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2885874	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4241437	0.87[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4856844	1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62254719	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62254723	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6548457	0.83[ASN][1000 genomes]
rs6548458	0.83[ASN][1000 genomes]
rs6548459	0.83[ASN][1000 genomes]
rs6548466	0.83[ASN][1000 genomes]
rs6548467	0.83[ASN][1000 genomes]
rs6548469	0.83[ASN][1000 genomes]
rs6795852	0.83[ASN][1000 genomes]
rs72914508	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs902323	0.90[CEU][hapmap]
rs902324	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs902326	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs969711	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9818912	0.87[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.82[MKK][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9838403	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs985345	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876253	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007093	chr3:67113534-67602973	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1490271	SNTN	cis	cerebellum	SCAN
rs1490271	SNTN	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67340800-67347200	Enhancers	HepG2	liver
2	chr3:67343000-67352200	Weak transcription	Aorta	Aorta
3	chr3:67343600-67345600	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:67343800-67346400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:67344800-67345400	Enhancers	Pancreatic Islets	Pancreatic Islet

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