Variant report

Variant	rs938011
Chromosome Location	chr11:57709997-57709998
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1113334	0.94[EUR][1000 genomes]
rs1113335	0.94[EUR][1000 genomes]
rs11600060	0.87[CEU][hapmap]
rs11601202	0.85[EUR][1000 genomes]
rs11601223	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11601663	0.85[EUR][1000 genomes]
rs11601841	0.87[CEU][hapmap];0.94[MEX][hapmap]
rs11602442	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11604473	0.87[CEU][hapmap]
rs11604630	0.87[CEU][hapmap]
rs11608016	0.85[EUR][1000 genomes]
rs12419176	0.97[EUR][1000 genomes]
rs12421773	0.95[EUR][1000 genomes]
rs12788836	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12790525	0.96[CEU][hapmap]
rs12792638	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12801976	0.95[EUR][1000 genomes]
rs12803905	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12804093	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1376489	0.96[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs1397273	0.96[EUR][1000 genomes]
rs17152364	0.87[MEX][hapmap]
rs17152376	0.87[CEU][hapmap];0.94[MEX][hapmap]
rs1814059	0.87[CEU][hapmap];0.94[MEX][hapmap]
rs1868881	0.83[MEX][hapmap]
rs2089747	0.94[EUR][1000 genomes]
rs2441952	0.81[CEU][hapmap]
rs34015013	0.88[EUR][1000 genomes]
rs34563263	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34594669	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35163247	0.90[EUR][1000 genomes]
rs35713433	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35742790	0.88[EUR][1000 genomes]
rs3853676	0.88[MEX][hapmap]
rs4509781	0.91[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap]
rs56055377	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs609154	0.94[EUR][1000 genomes]
rs61905309	0.95[EUR][1000 genomes]
rs66813766	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7109912	0.97[EUR][1000 genomes]
rs7113760	0.91[CEU][hapmap]
rs7120442	0.87[CEU][hapmap];0.94[MEX][hapmap]
rs7121128	0.94[EUR][1000 genomes]
rs7123570	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7126334	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs714942	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7926878	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7927022	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7929515	0.85[EUR][1000 genomes]
rs7930102	0.96[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs7930234	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7934184	0.87[CEU][hapmap];0.94[MEX][hapmap]
rs7935428	0.87[CEU][hapmap];0.94[MEX][hapmap]
rs7936212	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7938062	0.87[CEU][hapmap];0.94[MEX][hapmap]
rs7950003	0.90[EUR][1000 genomes]
rs930703	0.87[CEU][hapmap];0.94[MEX][hapmap]

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	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	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
4	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs938011	MS4A7	cis	parietal	SCAN
rs938011	YPEL4	cis	multi-tissue	Pritchard
rs938011	UBE2L6	cis	parietal	SCAN
rs938011	OR5M8	cis	cerebellum	SCAN
rs938011	DDB1	cis	cerebellum	SCAN
rs938011	MS4A10	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57707400-57710600	Enhancers	NHEK	skin
2	chr11:57707600-57710600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr11:57707600-57710600	Enhancers	HepG2	liver
4	chr11:57709400-57710200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:57709400-57710600	Enhancers	Esophagus	oesophagus
6	chr11:57709600-57710400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:57709800-57713400	Weak transcription	Lung	lung

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