Variant report

Variant	rs11602535
Chromosome Location	chr11:59190499-59190500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:59190460-59190610	GM12873	blood:	n/a	n/a

Variant related genes	Relation type
OR5A2	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1026320	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11602856	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11604452	0.81[GIH][hapmap];0.85[TSI][hapmap]
rs11605288	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11605552	0.82[EUR][1000 genomes]
rs11605572	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs11606927	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11606980	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12418613	0.80[EUR][1000 genomes]
rs12420159	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12420443	0.80[EUR][1000 genomes]
rs12420477	0.80[EUR][1000 genomes]
rs12785234	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12787182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12801196	0.80[EUR][1000 genomes]
rs12806497	0.81[EUR][1000 genomes]
rs12808401	0.81[EUR][1000 genomes]
rs12808731	0.80[EUR][1000 genomes]
rs1349777	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1453541	0.80[CEU][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs1453542	0.81[GIH][hapmap];0.85[TSI][hapmap]
rs1453544	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1453547	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1453549	0.81[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1453550	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1453551	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1453552	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1522759	0.84[TSI][hapmap]
rs1589601	0.80[EUR][1000 genomes]
rs17498652	0.80[EUR][1000 genomes]
rs17500478	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17584022	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17591107	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1901855	0.84[EUR][1000 genomes]
rs1955070	0.80[EUR][1000 genomes]
rs2167923	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2198451	0.82[EUR][1000 genomes]
rs2867731	0.81[EUR][1000 genomes]
rs2867748	0.81[EUR][1000 genomes]
rs34037092	0.80[EUR][1000 genomes]
rs35630700	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35872497	0.81[EUR][1000 genomes]
rs4938916	0.84[TSI][hapmap]
rs61901576	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61901620	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61902489	0.81[EUR][1000 genomes]
rs61902558	0.82[EUR][1000 genomes]
rs6591536	0.80[CEU][hapmap];0.83[TSI][hapmap]
rs7119928	0.81[EUR][1000 genomes]
rs7120797	0.81[EUR][1000 genomes]
rs7121582	0.81[TSI][hapmap]
rs7934882	0.80[EUR][1000 genomes]
rs7935959	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7947471	0.81[EUR][1000 genomes]
rs896877	0.81[EUR][1000 genomes]
rs896878	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs9665874	0.81[EUR][1000 genomes]
rs9787928	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9988851	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1046084	chr11:59034871-59314519	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1047952	chr11:59124719-59221606	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11602535	OR5AR1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59187400-59191200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:59189600-59190600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr11:59190000-59190600	Enhancers	Primary B cells from peripheral blood	blood
4	chr11:59190000-59190600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr11:59190400-59191400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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