Variant report

Variant	rs12309639
Chromosome Location	chr12:44672386-44672387
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IRAK4-4	chr12:44671035-44673934	ncRnaDb_ncrna_FR115916_1

Extended variants
information (count: 197 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:194)

rs_ID	r²[population]
rs10047523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1032886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10506235	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10506236	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10506237	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10506239	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10506240	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10506241	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10880622	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880628	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1115423	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11182417	0.86[ASN][1000 genomes]
rs11182423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11182430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11182431	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11182432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11182442	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11182443	1.00[JPT][hapmap]
rs11182449	1.00[JPT][hapmap]
rs11182453	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11182455	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1155808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1159252	1.00[CEU][hapmap]
rs11609283	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11609568	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11610433	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11612257	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11612946	1.00[CEU][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs11613064	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11613444	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11613902	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11615473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168078	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11830719	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11832219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11832828	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11832859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11834667	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11835507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12099982	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12297689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12297754	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12297933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12299030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299937	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12300793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12307454	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12307560	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12308449	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12308508	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12308569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12314470	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12315961	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12319009	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1352935	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1527316	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1643429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1643431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1701088	0.92[ASN][1000 genomes]
rs17094062	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17094063	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17094092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17094117	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17094121	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17094169	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17094183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17094226	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17094227	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17094228	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17094231	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17094235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17094242	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17094260	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17094263	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17094282	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17094291	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17094292	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17094298	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17094299	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17094300	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17094304	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17094313	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17094322	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17094323	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17094325	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17094328	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17094330	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17094336	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17094344	1.00[JPT][hapmap]
rs17121305	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17121310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2032782	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2062952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs2062954	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2112147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2174508	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2638853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2657576	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2657577	0.92[ASN][1000 genomes]
rs28397962	0.87[EUR][1000 genomes]
rs28538835	0.87[EUR][1000 genomes]
rs28838075	0.91[EUR][1000 genomes]
rs4631946	0.88[CEU][hapmap]
rs55633842	0.87[EUR][1000 genomes]
rs55645887	0.87[EUR][1000 genomes]
rs55649839	0.84[EUR][1000 genomes]
rs55747421	0.87[EUR][1000 genomes]
rs55782485	0.88[EUR][1000 genomes]
rs55874183	0.86[EUR][1000 genomes]
rs55950371	0.84[EUR][1000 genomes]
rs55977905	0.88[EUR][1000 genomes]
rs55991202	0.87[EUR][1000 genomes]
rs55999021	0.81[EUR][1000 genomes]
rs56134810	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56192803	0.87[EUR][1000 genomes]
rs56218625	0.81[EUR][1000 genomes]
rs56339470	0.84[EUR][1000 genomes]
rs57010132	0.86[EUR][1000 genomes]
rs57094207	0.85[EUR][1000 genomes]
rs57907832	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58206004	0.86[EUR][1000 genomes]
rs58450697	0.85[EUR][1000 genomes]
rs59118688	0.87[ASN][1000 genomes]
rs59136483	0.87[EUR][1000 genomes]
rs59152420	0.95[EUR][1000 genomes]
rs59375742	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59477802	0.86[EUR][1000 genomes]
rs59628873	0.93[EUR][1000 genomes]
rs59704299	0.83[EUR][1000 genomes]
rs59957474	0.87[EUR][1000 genomes]
rs60008417	0.91[EUR][1000 genomes]
rs60461380	0.87[EUR][1000 genomes]
rs60995491	0.86[EUR][1000 genomes]
rs61228557	0.87[EUR][1000 genomes]
rs61629163	0.90[EUR][1000 genomes]
rs61690882	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6582497	0.83[EUR][1000 genomes]
rs6582498	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs66970043	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67184817	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67713366	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs68049983	0.93[EUR][1000 genomes]
rs7137469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137787	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7139362	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7295281	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7295832	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7297563	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7305976	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7306362	0.86[EUR][1000 genomes]
rs7306647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7308476	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs73093458	0.81[EUR][1000 genomes]
rs73093474	0.86[EUR][1000 genomes]
rs73094803	0.86[EUR][1000 genomes]
rs73099009	0.80[EUR][1000 genomes]
rs73099011	0.80[EUR][1000 genomes]
rs73099027	0.85[EUR][1000 genomes]
rs73100803	0.85[EUR][1000 genomes]
rs73100825	0.90[EUR][1000 genomes]
rs73100829	0.84[EUR][1000 genomes]
rs73100834	0.91[EUR][1000 genomes]
rs73100841	0.84[EUR][1000 genomes]
rs73100848	0.87[EUR][1000 genomes]
rs73102910	0.86[EUR][1000 genomes]
rs73102919	0.87[EUR][1000 genomes]
rs73102924	0.87[EUR][1000 genomes]
rs73102925	0.87[EUR][1000 genomes]
rs73102927	0.87[EUR][1000 genomes]
rs73102932	0.87[EUR][1000 genomes]
rs73102937	0.83[EUR][1000 genomes]
rs73102938	0.87[EUR][1000 genomes]
rs7310881	0.85[EUR][1000 genomes]
rs7311714	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7312930	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7313269	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7315208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7316737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73288050	0.93[EUR][1000 genomes]
rs7954216	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7961974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7967957	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7968777	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7969885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7971340	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7976652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7977539	1.00[JPT][hapmap]
rs7980383	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs860867	0.87[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs963095	0.91[EUR][1000 genomes]
rs9738149	1.00[CEU][hapmap];0.83[EUR][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	nsv1049818	chr12:44486312-45133783	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv832393	chr12:44529406-44692414	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv686	chr12:44671240-44696910	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	lncRNA	n/a	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44654200-44679400	Weak transcription	Pancreas	Pancrea
2	chr12:44671800-44672800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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