Variant report

Variant	rs1879929
Chromosome Location	chr11:59184192-59184193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10792231	0.82[JPT][hapmap]
rs11229957	0.85[EUR][1000 genomes]
rs11229958	0.85[EUR][1000 genomes]
rs11604216	0.99[EUR][1000 genomes]
rs11604452	0.83[CEU][hapmap];0.91[TSI][hapmap]
rs12417674	0.82[EUR][1000 genomes]
rs12418613	0.84[EUR][1000 genomes]
rs12419033	0.82[EUR][1000 genomes]
rs12419445	0.82[EUR][1000 genomes]
rs12420443	0.84[EUR][1000 genomes]
rs12420477	0.84[EUR][1000 genomes]
rs12801196	0.84[EUR][1000 genomes]
rs12806497	0.85[EUR][1000 genomes]
rs12808401	0.85[EUR][1000 genomes]
rs12808731	0.84[EUR][1000 genomes]
rs1349777	0.84[TSI][hapmap]
rs1453541	0.88[TSI][hapmap]
rs1453542	0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs1453544	0.81[TSI][hapmap]
rs1453547	0.84[TSI][hapmap]
rs1453550	0.84[TSI][hapmap]
rs1453551	0.84[TSI][hapmap]
rs1522759	0.84[TSI][hapmap]
rs1589600	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1589601	0.84[EUR][1000 genomes]
rs1608210	0.85[EUR][1000 genomes]
rs1608211	0.85[EUR][1000 genomes]
rs1608212	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17498652	0.84[EUR][1000 genomes]
rs17584022	0.81[TSI][hapmap]
rs17591107	0.81[TSI][hapmap]
rs1851513	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1901856	0.85[EUR][1000 genomes]
rs1955070	0.84[EUR][1000 genomes]
rs1972149	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2040326	0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs2091008	0.85[EUR][1000 genomes]
rs2123675	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2123676	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2198451	0.87[EUR][1000 genomes]
rs34037092	0.84[EUR][1000 genomes]
rs34387009	0.83[EUR][1000 genomes]
rs34730029	0.82[EUR][1000 genomes]
rs35872497	0.85[EUR][1000 genomes]
rs4536240	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4938916	0.84[TSI][hapmap]
rs4939272	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4939291	0.85[EUR][1000 genomes]
rs61902489	0.85[EUR][1000 genomes]
rs61902558	0.86[EUR][1000 genomes]
rs61902559	0.99[EUR][1000 genomes]
rs61904597	0.82[EUR][1000 genomes]
rs6591536	0.83[TSI][hapmap]
rs7103331	0.82[EUR][1000 genomes]
rs7105556	0.88[CEU][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs7121582	0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7934882	0.84[EUR][1000 genomes]
rs7944892	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7949055	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7952071	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv541052	chr11:59119390-59185103	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1879929	OR5D13	cis	cerebellum	SCAN
rs1879929	SERPING1	cis	cerebellum	SCAN
rs1879929	DDB1	cis	parietal	SCAN
rs1879929	SNORD27	cis	parietal	SCAN
rs1879929	OR5AR1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59181600-59184200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:59182400-59186000	Enhancers	Primary B cells from peripheral blood	blood
3	chr11:59182800-59187200	Enhancers	Fetal Brain Male	brain
4	chr11:59183400-59184800	Enhancers	Primary B cells from cord blood	blood
5	chr11:59183600-59185000	Enhancers	Fetal Thymus	thymus
6	chr11:59184000-59184200	Enhancers	Primary T cells from cord blood	blood
7	chr11:59184000-59185000	Weak transcription	Fetal Brain Female	brain

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