Variant report

Variant	rs12517690
Chromosome Location	chr5:44939293-44939294
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 144 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10038562	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10040082	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10040488	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10041518	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10044096	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10045264	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10054773	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10057521	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10059086	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10060878	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10063172	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10064437	0.87[EUR][1000 genomes]
rs10065638	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10069220	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10070037	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10072025	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10072259	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10462080	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10462081	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10462082	0.80[ASN][1000 genomes]
rs10462083	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10473376	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10473377	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1048758	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1061310	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11741772	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11746506	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11747159	0.83[EUR][1000 genomes]
rs11750119	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11948387	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11948636	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11949847	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11951760	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11957920	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11958451	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11958808	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12109710	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12188871	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12513749	0.90[EUR][1000 genomes]
rs12518851	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12651949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12652026	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12656984	0.89[EUR][1000 genomes]
rs13154781	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13155698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13157608	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13159598	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs13168400	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13174122	0.95[CEU][hapmap];0.91[CHB][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13177711	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13183209	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13185174	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13187933	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13189120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1371023	0.81[ASN][1000 genomes]
rs1371024	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1371025	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1438819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1438820	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1438822	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1438827	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16901963	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16901964	0.89[EUR][1000 genomes]
rs16901965	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16901989	0.90[EUR][1000 genomes]
rs16901990	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1866406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2083243	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2165008	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2330619	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2330620	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34501299	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3747479	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3761648	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3761649	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3761650	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4129642	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4329028	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4395640	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4412123	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4457088	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4457089	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4518409	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4596389	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4629607	0.85[EUR][1000 genomes]
rs4642377	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4866783	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4866784	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4866920	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57300972	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6451772	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6451774	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6451775	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6451781	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67274820	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6859157	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6867533	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap]
rs6868232	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6868779	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6870136	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6871820	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6872254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6875287	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6875933	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6881563	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6894324	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6896350	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6896417	0.80[ASN][1000 genomes]
rs71610376	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs727304	0.90[CHB][hapmap];0.84[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs727305	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs729599	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7703059	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7703618	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7705343	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7708506	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7710952	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7710978	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7711136	0.80[ASN][1000 genomes]
rs7712949	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7715731	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7716571	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7717459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7720787	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs7728431	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7730841	0.80[ASN][1000 genomes]
rs7736952	0.90[EUR][1000 genomes]
rs9292913	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9292914	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9292915	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs930394	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9637783	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9637796	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9637797	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs969679	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9790879	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9790896	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9791056	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9791059	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9791164	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs987394	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027897	chr5:44695278-45061623	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv880397	chr5:44800665-44939293	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv880483	chr5:44827292-45038026	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12517690	LOC647121	Cis_chr	lymphoblastoid	RTeQTL
rs12517690	MRPS30	cis	cerebellum	SCAN
rs12517690	MRPS30	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:44938600-44941200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:44939200-44939600	Enhancers	Hela-S3	cervix

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