Variant report

Variant	rs9952836
Chromosome Location	chr18:13352704-13352705
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1107341	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11080646	0.82[GIH][hapmap];0.82[MEX][hapmap]
rs11659711	0.90[EUR][1000 genomes]
rs11659822	0.91[EUR][1000 genomes]
rs11661280	0.91[EUR][1000 genomes]
rs11665476	0.90[EUR][1000 genomes]
rs12456859	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12456874	1.00[CEU][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs12604142	0.84[JPT][hapmap]
rs12955917	0.92[EUR][1000 genomes]
rs12961452	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1454128	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16940349	0.90[CEU][hapmap];0.95[MEX][hapmap]
rs17681406	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1840267	0.92[EUR][1000 genomes]
rs1869497	0.90[CEU][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap]
rs1893980	0.83[CEU][hapmap]
rs2085050	0.88[CEU][hapmap]
rs2187502	0.90[CEU][hapmap];0.90[MEX][hapmap]
rs2276392	0.90[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs2867874	0.89[CEU][hapmap]
rs4570935	0.89[CEU][hapmap]
rs6505808	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7226901	0.89[CEU][hapmap]
rs7227361	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7231366	0.82[MEX][hapmap]
rs7234501	0.85[CEU][hapmap]
rs7234675	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7236152	0.89[CEU][hapmap]
rs7237577	0.82[GIH][hapmap];0.82[MEX][hapmap]
rs7241109	0.90[CEU][hapmap]
rs7241410	0.90[CEU][hapmap]
rs7241438	0.90[CEU][hapmap];0.95[MEX][hapmap]
rs8087505	0.90[CEU][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs8088874	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8092304	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8094197	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs897035	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs897036	0.90[JPT][hapmap]
rs930797	0.90[CEU][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs930798	0.90[CEU][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs930799	0.85[CEU][hapmap];0.86[MEX][hapmap]
rs949259	0.90[CEU][hapmap]
rs9947830	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9948620	0.92[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9954359	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs9957335	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9957621	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9960893	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9963572	0.94[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][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
rs9952836	TUBB6	cis	cerebellum	SCAN
rs9952836	AFG3L2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13349200-13353200	Weak transcription	Thymus	Thymus
2	chr18:13351600-13353200	Enhancers	Dnd41	blood
3	chr18:13351800-13374800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr18:13352400-13353200	Enhancers	Primary T cells from cord blood	blood
5	chr18:13352400-13353600	Enhancers	Liver	Liver
6	chr18:13352400-13355000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr18:13352600-13354200	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr18:13352600-13354400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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