Variant report

Variant	rs11742249
Chromosome Location	chr5:41952292-41952293
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10941559	0.83[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11738517	0.81[EUR][1000 genomes]
rs11739106	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11739257	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs11740524	0.89[EUR][1000 genomes]
rs11740946	0.87[EUR][1000 genomes]
rs11744279	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs11744516	0.87[EUR][1000 genomes]
rs11744623	0.90[EUR][1000 genomes]
rs11746511	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11747881	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11747921	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs11749008	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11750607	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs11750760	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11750790	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13153468	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13153837	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13156367	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13162040	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13163137	0.87[EUR][1000 genomes]
rs13164201	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13165731	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13167578	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13168035	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13169977	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13170096	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13176368	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13177937	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13179852	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13180405	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13182336	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13185973	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1508815	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1508818	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs16871955	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16871972	0.89[EUR][1000 genomes]
rs16900142	0.83[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1876653	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1876654	0.88[EUR][1000 genomes]
rs33967331	0.87[EUR][1000 genomes]
rs34071445	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34329864	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34339137	0.87[EUR][1000 genomes]
rs34369972	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34412181	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34500930	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34569700	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34625465	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34663371	0.87[EUR][1000 genomes]
rs34841703	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34873414	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35077044	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs35244816	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35252930	0.87[EUR][1000 genomes]
rs35343042	0.86[EUR][1000 genomes]
rs35613904	0.90[EUR][1000 genomes]
rs35748945	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35764180	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35861205	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36005620	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36009913	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36113900	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3926618	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4957430	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs55817686	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56017638	0.87[EUR][1000 genomes]
rs60209308	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs66820325	0.89[EUR][1000 genomes]
rs67114999	0.87[EUR][1000 genomes]
rs67206815	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67715253	0.86[EUR][1000 genomes]
rs67869805	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6865448	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6866549	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6879341	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6881206	0.97[EUR][1000 genomes]
rs6881873	0.89[EUR][1000 genomes]
rs6883144	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6888816	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6889217	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs72746918	0.86[EUR][1000 genomes]
rs72746919	0.86[EUR][1000 genomes]
rs72746957	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7709500	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7712911	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs7713580	0.82[YRI][hapmap]
rs7721136	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7724934	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7725264	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs951883	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs964267	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9687619	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830272	chr5:41833365-41986167	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
2	nsv830273	chr5:41867296-42066070	Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
3	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
4	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11742249	OXCT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41952000-41956800	Weak transcription	Aorta	Aorta
2	chr5:41952200-41956400	Weak transcription	Gastric	stomach

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