Variant report

Variant	rs10840089
Chromosome Location	chr11:8622855-8622856
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10160430	0.82[AMR][1000 genomes]
rs10160804	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10160805	0.82[AMR][1000 genomes]
rs10743078	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10743079	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10743080	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743081	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10743082	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769908	0.84[MEX][hapmap]
rs10769915	0.82[AMR][1000 genomes]
rs10769916	0.82[AMR][1000 genomes]
rs10769918	0.93[ASN][1000 genomes]
rs10769919	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10769920	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10769921	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10769922	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10769923	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769924	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10769925	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10769926	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10769927	0.91[ASN][1000 genomes]
rs10769929	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10769936	0.83[MEX][hapmap]
rs10840062	0.80[CEU][hapmap]
rs10840077	0.82[AMR][1000 genomes]
rs10840079	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840080	0.81[AMR][1000 genomes]
rs10840081	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10840083	0.81[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10840084	0.83[AMR][1000 genomes]
rs10840085	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10840087	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10840091	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11041929	0.96[CEU][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs11041978	0.80[CHD][hapmap];0.84[MEX][hapmap]
rs11041982	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs11041986	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11041990	0.81[CEU][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11041993	0.88[ASN][1000 genomes]
rs11041994	0.81[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11041995	0.81[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11041997	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11041999	0.81[AMR][1000 genomes]
rs11042002	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12226478	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12785939	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12805671	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12806736	0.96[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap]
rs1374263	0.84[EUR][1000 genomes]
rs1446464	0.96[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs1900272	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2028882	0.84[MEX][hapmap]
rs2289921	0.80[CEU][hapmap]
rs2289923	0.96[CEU][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs2871753	0.81[CEU][hapmap]
rs4131072	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4244804	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4244806	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4291677	0.83[MEX][hapmap]
rs4344491	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4405311	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4418812	0.83[AMR][1000 genomes]
rs4475924	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4520598	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4612809	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4620720	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4758067	0.96[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs4929929	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4929941	1.00[ASW][hapmap];0.96[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];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4929942	0.87[CHB][hapmap];0.83[CHD][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4929943	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4929944	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4929945	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4929949	0.83[AMR][1000 genomes]
rs4929950	0.96[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6484485	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7126013	0.95[CEU][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs7126934	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs7129357	0.85[EUR][1000 genomes]
rs725502	0.84[MEX][hapmap]
rs726007	0.96[CEU][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs7929120	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7931604	0.96[CEU][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs7934396	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7939731	0.84[MEX][hapmap]
rs885114	0.83[MEX][hapmap]
rs9284150	0.96[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9284151	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9300088	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9300089	0.87[CEU][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9300091	0.81[CEU][hapmap]
rs9300092	0.84[MEX][hapmap]
rs9300094	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs935370	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs9705083	0.81[CEU][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9705253	0.82[AMR][1000 genomes]
rs9736791	0.83[CHD][hapmap];0.84[MEX][hapmap]
rs9737312	0.81[CEU][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751035	chr11:8431654-8685451	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv896983	chr11:8526643-8682465	ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10840089	RPL27A	cis	cerebellum	SCAN
rs10840089	RPL27A	cis	parietal	SCAN
rs10840089	SNORA45	cis	parietal	SCAN
rs10840089	ST5	cis	cerebellum	SCAN
rs10840089	STK33	cis	cerebellum	SCAN
rs10840089	ZNF616	trans	parietal	SCAN
rs10840089	C11orf17	cis	multi-tissue	Pritchard
rs10840089	STK33	cis	parietal	SCAN
rs10840089	STK33	cis	Artery Tibial	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8616600-8625600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr11:8617000-8625400	Weak transcription	GM12878-XiMat	blood
3	chr11:8618400-8623000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:8619000-8623000	Weak transcription	A549	lung
5	chr11:8619600-8625200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:8622800-8623400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr11:8622800-8623600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:8622800-8623600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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