Variant report

Variant	rs1225
Chromosome Location	chr18:13337559-13337560
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10084046	0.87[JPT][hapmap]
rs1107340	0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11080642	1.00[JPT][hapmap]
rs12959091	0.85[JPT][hapmap]
rs12960927	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16940343	0.87[JPT][hapmap]
rs16940349	0.83[JPT][hapmap]
rs2085049	1.00[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2085050	0.87[JPT][hapmap]
rs2187502	0.87[JPT][hapmap]
rs2276392	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2867874	0.83[JPT][hapmap]
rs2867878	1.00[ASW][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.80[AMR][1000 genomes]
rs35664252	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35815061	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3960634	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4570934	0.87[JPT][hapmap]
rs4570935	0.83[JPT][hapmap]
rs4797760	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4797761	1.00[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4797764	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4797765	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505798	0.87[JPT][hapmap]
rs6505810	0.91[MEX][hapmap]
rs7226901	0.90[JPT][hapmap]
rs7231366	0.83[JPT][hapmap]
rs7234501	0.87[JPT][hapmap]
rs7236152	0.89[JPT][hapmap]
rs7241109	0.83[JPT][hapmap]
rs7241438	0.83[JPT][hapmap]
rs7242024	0.83[JPT][hapmap]
rs7242140	0.83[JPT][hapmap]
rs8087505	0.87[JPT][hapmap]
rs8094197	0.87[JPT][hapmap]
rs930797	0.83[JPT][hapmap]
rs930798	0.83[JPT][hapmap]
rs930799	0.83[JPT][hapmap]
rs949259	0.83[JPT][hapmap]
rs9946524	0.86[JPT][hapmap]
rs9953274	0.87[JPT][hapmap]
rs9954359	0.95[JPT][hapmap];0.83[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	nsv531246	chr18:13298774-14082028	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1225	AFG3L2	cis	cerebellum	SCAN
rs1225	IMPA2	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13320400-13338200	Weak transcription	Small Intestine	intestine
2	chr18:13332000-13337600	Weak transcription	Thymus	Thymus
3	chr18:13336400-13338800	Weak transcription	Fetal Thymus	thymus
4	chr18:13336800-13337800	Enhancers	HepG2	liver
5	chr18:13337000-13337600	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr18:13337200-13338400	Flanking Active TSS	Liver	Liver
7	chr18:13337200-13338600	Enhancers	Left Ventricle	heart
8	chr18:13337400-13338800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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