Variant report

Variant	rs2276392
Chromosome Location	chr18:13336841-13336842
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10084046	0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs1107340	0.82[JPT][hapmap]
rs11080642	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11080646	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs11659711	0.85[EUR][1000 genomes]
rs11659822	0.84[EUR][1000 genomes]
rs11661280	0.82[EUR][1000 genomes]
rs11665476	0.85[EUR][1000 genomes]
rs1225	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12456859	0.86[EUR][1000 genomes]
rs12456874	0.90[CEU][hapmap];0.82[TSI][hapmap]
rs12955917	0.83[EUR][1000 genomes]
rs12959077	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12959091	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12960927	0.81[ASN][1000 genomes]
rs1454128	0.87[EUR][1000 genomes]
rs16940343	0.82[JPT][hapmap]
rs16940349	0.90[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs1840267	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1869497	0.90[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs1893980	0.84[CEU][hapmap]
rs2085048	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2085049	0.95[JPT][hapmap]
rs2085050	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2187501	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2187502	0.90[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2867874	0.90[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs2867875	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2867876	0.83[ASN][1000 genomes]
rs2867878	0.83[MEX][hapmap]
rs4570934	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs4570935	0.89[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs4602105	0.83[ASN][1000 genomes]
rs4606791	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4797761	0.95[JPT][hapmap]
rs4797764	0.82[JPT][hapmap]
rs6505798	0.82[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.80[ASN][1000 genomes]
rs6505802	0.83[ASN][1000 genomes]
rs6505803	0.91[ASN][1000 genomes]
rs6505807	0.81[ASN][1000 genomes]
rs6505810	0.83[MEX][hapmap]
rs7226901	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7227361	0.95[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs7230643	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7231366	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7231701	0.81[EUR][1000 genomes]
rs7234501	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7234675	0.80[EUR][1000 genomes]
rs7236152	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7236934	0.90[ASN][1000 genomes]
rs7237181	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7237577	0.82[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.80[ASN][1000 genomes]
rs7241109	0.90[CEU][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs7241410	0.90[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs7241438	0.90[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs7242024	0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs7242140	0.91[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs7242207	0.82[EUR][1000 genomes]
rs7242230	0.82[EUR][1000 genomes]
rs8087505	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8088874	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8092304	0.92[EUR][1000 genomes]
rs8094197	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs897035	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs9303783	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs930797	0.90[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs930798	0.90[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs930799	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs949259	0.90[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs981621	0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs9946524	0.86[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9952682	0.87[ASN][1000 genomes]
rs9952836	0.90[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs9953274	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs9954359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9954816	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9957334	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9957335	0.86[EUR][1000 genomes]
rs9957621	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs9960893	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9963572	0.84[CEU][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2276392	AFG3L2	cis	cerebellum	SCAN

Chromatin state (count:7 , 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	chr18:13336200-13337000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr18:13336200-13337200	Weak transcription	Left Ventricle	heart
5	chr18:13336400-13338800	Weak transcription	Fetal Thymus	thymus
6	chr18:13336600-13337200	Enhancers	Liver	Liver
7	chr18:13336800-13337800	Enhancers	HepG2	liver

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