Variant report

Variant	rs11229171
Chromosome Location	chr11:57707610-57707611
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10792118	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11229170	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11229172	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11229173	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229183	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11512731	0.87[ASN][1000 genomes]
rs11512732	0.84[ASN][1000 genomes]
rs12366063	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12420220	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1510418	0.81[EUR][1000 genomes]
rs1848879	0.86[EUR][1000 genomes]
rs34419144	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35241049	0.81[EUR][1000 genomes]
rs35994197	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4245215	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4272798	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs588713	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs591322	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs593239	0.85[EUR][1000 genomes]
rs600488	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs602861	1.00[CEU][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs606731	0.89[EUR][1000 genomes]
rs615133	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs616911	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61905278	0.91[ASN][1000 genomes]
rs626043	0.85[EUR][1000 genomes]
rs633129	0.86[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs636388	0.85[EUR][1000 genomes]
rs6591443	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662638	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs681397	0.90[EUR][1000 genomes]
rs7103977	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7106195	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7119973	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71484480	0.87[ASN][1000 genomes]
rs7926999	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7943793	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][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	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11229171	OR4D11	cis	parietal	SCAN
rs11229171	MS4A2	cis	cerebellum	SCAN
rs11229171	YPEL4	cis	lung	GTEx
rs11229171	YPEL4	cis	multi-tissue	Pritchard
rs11229171	TIMM10	cis	parietal	SCAN
rs11229171	TIMM10	cis	multi-tissue	Pritchard
rs11229171	OR4C6	cis	parietal	SCAN
rs11229171	UBE2L6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57707400-57710600	Enhancers	NHEK	skin
2	chr11:57707600-57707800	Enhancers	Esophagus	oesophagus
3	chr11:57707600-57709600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:57707600-57710600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:57707600-57710600	Enhancers	HepG2	liver

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