Variant report

Variant	rs10940090
Chromosome Location	chr5:49452155-49452156
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10053631	0.94[ASN][1000 genomes]
rs10053639	0.93[ASN][1000 genomes]
rs10054827	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10057362	0.88[AMR][1000 genomes]
rs10062087	0.88[AMR][1000 genomes]
rs10067381	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10471767	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10471784	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10940514	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10940520	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10940533	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10940646	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11514621	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11740458	0.91[ASN][1000 genomes]
rs11742067	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11747651	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11748483	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11749165	0.88[AMR][1000 genomes]
rs11950947	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11950949	0.82[ASN][1000 genomes]
rs11953016	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11953045	0.82[ASN][1000 genomes]
rs12188257	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12513792	0.83[EUR][1000 genomes]
rs12515555	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12517502	0.83[AMR][1000 genomes]
rs12521033	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12521333	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12521903	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13155708	0.83[AMR][1000 genomes]
rs13160767	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13175165	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13178037	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13358828	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2125456	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2168920	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2168922	0.84[ASN][1000 genomes]
rs2199089	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2199090	0.83[AMR][1000 genomes]
rs2199093	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2199098	0.83[AMR][1000 genomes]
rs2219451	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2219452	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2219453	0.89[AMR][1000 genomes]
rs2353222	0.93[ASN][1000 genomes]
rs35295454	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4249603	0.95[ASN][1000 genomes]
rs4250105	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4250165	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4302633	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4305678	0.93[AMR][1000 genomes]
rs4308516	0.84[AMR][1000 genomes]
rs4379243	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4415115	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4446513	0.95[ASN][1000 genomes]
rs4554275	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs473120	0.86[AMR][1000 genomes]
rs482120	0.90[AMR][1000 genomes]
rs485101	0.88[AMR][1000 genomes]
rs4865549	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4865550	0.95[ASN][1000 genomes]
rs4865551	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4865552	0.92[ASN][1000 genomes]
rs4865567	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4865637	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4865722	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4865723	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4865727	0.90[ASN][1000 genomes]
rs4865728	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4865761	0.88[AMR][1000 genomes]
rs4865778	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4865799	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4865801	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4865803	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4865966	0.83[AMR][1000 genomes]
rs4866006	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs504520	0.85[AMR][1000 genomes]
rs528968	0.87[AMR][1000 genomes]
rs531198	0.90[AMR][1000 genomes]
rs534123	0.92[AMR][1000 genomes]
rs535113	0.81[AMR][1000 genomes]
rs547563	0.85[AMR][1000 genomes]
rs55815545	0.88[ASN][1000 genomes]
rs559096	0.90[AMR][1000 genomes]
rs560861	0.85[AMR][1000 genomes]
rs561028	0.80[AMR][1000 genomes]
rs564641	0.85[AMR][1000 genomes]
rs7293304	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7293312	0.86[EUR][1000 genomes]
rs7293339	0.90[AMR][1000 genomes]
rs7293348	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7293351	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7293378	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7293410	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7293414	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7293422	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7293432	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7293476	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7293501	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8175378	0.91[ASN][1000 genomes]
rs8185119	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8185347	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8188005	0.81[AMR][1000 genomes]
rs8188146	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8188195	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8188203	0.95[ASN][1000 genomes]
rs8188210	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8188289	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9688065	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9688258	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9800133	0.80[AMR][1000 genomes]
rs9800135	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9800240	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	nsv830285	chr5:49445361-49527825	ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv598092	chr5:49448027-49514368	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10940090	EMB	cis	Whole Blood	GTEx
rs10940090	EMB	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49451000-49456000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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