Variant report

Variant	rs11740458
Chromosome Location	chr5:49444316-49444317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10053631	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10053639	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10054827	0.88[ASN][1000 genomes]
rs10067381	0.97[ASN][1000 genomes]
rs10079057	0.80[AMR][1000 genomes]
rs10471767	0.90[ASN][1000 genomes]
rs10471784	0.90[ASN][1000 genomes]
rs10940090	0.91[ASN][1000 genomes]
rs10940514	0.92[ASN][1000 genomes]
rs10940520	0.92[ASN][1000 genomes]
rs10940533	0.97[ASN][1000 genomes]
rs10940646	0.91[ASN][1000 genomes]
rs11748483	0.86[ASN][1000 genomes]
rs11950949	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11953016	0.88[ASN][1000 genomes]
rs11953045	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12188257	0.92[ASN][1000 genomes]
rs12520167	0.83[AMR][1000 genomes]
rs12521033	0.91[ASN][1000 genomes]
rs12521333	0.85[ASN][1000 genomes]
rs12521903	0.92[ASN][1000 genomes]
rs12523073	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12655271	0.83[AMR][1000 genomes]
rs13160767	0.91[ASN][1000 genomes]
rs13175165	0.91[ASN][1000 genomes]
rs1328254	0.80[AMR][1000 genomes]
rs2125464	0.82[AMR][1000 genomes]
rs2168922	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2353222	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35295454	0.83[ASN][1000 genomes]
rs4249603	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4250105	0.83[ASN][1000 genomes]
rs4250165	0.89[ASN][1000 genomes]
rs4302633	0.84[ASN][1000 genomes]
rs4379243	0.92[ASN][1000 genomes]
rs4415115	0.92[ASN][1000 genomes]
rs4446513	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs472278	0.83[AMR][1000 genomes]
rs4865549	0.89[ASN][1000 genomes]
rs4865550	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4865551	0.88[ASN][1000 genomes]
rs4865552	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4865727	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4865728	0.91[ASN][1000 genomes]
rs4865778	0.93[ASN][1000 genomes]
rs4865799	0.83[ASN][1000 genomes]
rs4865801	0.95[ASN][1000 genomes]
rs4866008	0.86[AMR][1000 genomes]
rs507396	0.80[AMR][1000 genomes]
rs527170	0.84[AMR][1000 genomes]
rs55815545	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7293378	0.83[ASN][1000 genomes]
rs7293410	0.91[ASN][1000 genomes]
rs7293414	0.90[ASN][1000 genomes]
rs7293422	0.93[ASN][1000 genomes]
rs7293501	0.86[ASN][1000 genomes]
rs8175378	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8185119	0.92[ASN][1000 genomes]
rs8188088	0.84[AMR][1000 genomes]
rs8188099	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs8188146	0.89[ASN][1000 genomes]
rs8188195	0.83[ASN][1000 genomes]
rs8188203	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8188217	0.82[AMR][1000 genomes]
rs8188289	0.91[ASN][1000 genomes]
rs9688065	0.92[ASN][1000 genomes]
rs9688258	0.97[ASN][1000 genomes]
rs9800135	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv19415	chr5:49405763-49485157	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	n/a	n/a	inside rSNPs	diseases
2	nsv820439	chr5:49405763-49552643	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv15107	chr5:49405763-49562327	Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv2760950	chr5:49432831-49624358	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv598089	chr5:49441601-49547088	ZNF genes & repeats Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv598090	chr5:49441966-49514368	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases
7	nsv598091	chr5:49441966-49547088	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11740458	EMB	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49441400-49447800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr5:49441400-49447800	Weak transcription	GM12878-XiMat	blood
3	chr5:49441400-49448800	Weak transcription	Fetal Heart	heart
4	chr5:49441400-49450400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:49441400-49450400	Weak transcription	Hela-S3	cervix
6	chr5:49441400-49450400	Weak transcription	NH-A	brain
7	chr5:49441400-49450400	Weak transcription	NHEK	skin
8	chr5:49441400-49450400	Weak transcription	Osteobl	bone

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