Variant report

Variant	rs602861
Chromosome Location	chr11:57687365-57687366
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10792118	0.89[EUR][1000 genomes]
rs11229170	0.89[EUR][1000 genomes]
rs11229171	0.89[EUR][1000 genomes]
rs11229172	0.88[EUR][1000 genomes]
rs11229173	0.87[EUR][1000 genomes]
rs11229183	0.86[EUR][1000 genomes]
rs12366063	0.86[EUR][1000 genomes]
rs12420220	0.86[EUR][1000 genomes]
rs4245215	0.87[EUR][1000 genomes]
rs588713	0.92[EUR][1000 genomes]
rs591322	0.94[EUR][1000 genomes]
rs593239	0.86[EUR][1000 genomes]
rs600488	0.94[EUR][1000 genomes]
rs606731	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs615133	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs616911	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs626043	0.85[EUR][1000 genomes]
rs633129	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs636388	0.86[EUR][1000 genomes]
rs6591443	0.87[EUR][1000 genomes]
rs662638	0.93[EUR][1000 genomes]
rs681397	0.91[EUR][1000 genomes]
rs7119973	0.87[EUR][1000 genomes]
rs7926999	0.81[EUR][1000 genomes]
rs7943793	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs602861	MS4A2	cis	cerebellum	SCAN
rs602861	YPEL4	cis	multi-tissue	Pritchard
rs602861	YPEL4	cis	lung	GTEx
rs602861	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs602861	TIMM10	cis	parietal	SCAN
rs602861	TIMM10	cis	multi-tissue	Pritchard
rs602861	OR4C6	cis	parietal	SCAN
rs602861	OR4D11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57680000-57687800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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