Variant report

Variant	rs1501513
Chromosome Location	chr5:42168682-42168683
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OXCT1-1	chr5:42168565-42168689	ENSG00000248519
2	lnc-OXCT1-1	chr5:42168565-42168689	XLOC_004800
3	lnc-OXCT1-1	chr5:42168565-42168689	XLOC_004800
4	lnc-OXCT1-1	chr5:42168565-42168689	XLOC_004800
5	lnc-FBXO4-1	chr5:42168564-42168689	NONHSAT101190
6	lnc-OXCT1-1	chr5:42168565-42168689	NR_104635

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10037143	0.99[EUR][1000 genomes]
rs10050512	0.88[EUR][1000 genomes]
rs10052738	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs10053179	0.81[AMR][1000 genomes]
rs10054119	0.83[EUR][1000 genomes]
rs10060873	0.99[EUR][1000 genomes]
rs10064990	0.98[EUR][1000 genomes]
rs10073423	0.88[EUR][1000 genomes]
rs10077609	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10078494	0.99[EUR][1000 genomes]
rs10079521	0.98[EUR][1000 genomes]
rs10461734	0.99[EUR][1000 genomes]
rs10461735	0.99[EUR][1000 genomes]
rs10461736	0.88[EUR][1000 genomes]
rs10462034	0.86[EUR][1000 genomes]
rs1073273	0.86[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1110874	1.00[EUR][1000 genomes]
rs11954853	0.95[EUR][1000 genomes]
rs12153093	0.88[EUR][1000 genomes]
rs13189999	0.87[EUR][1000 genomes]
rs1354108	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1501516	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1501517	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1501518	0.99[EUR][1000 genomes]
rs1501519	0.99[EUR][1000 genomes]
rs1827329	0.98[EUR][1000 genomes]
rs1827330	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1827331	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1875430	1.00[EUR][1000 genomes]
rs1909951	0.98[EUR][1000 genomes]
rs1995351	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2134102	0.86[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs34035285	0.85[EUR][1000 genomes]
rs34813199	0.83[EUR][1000 genomes]
rs35005365	0.85[EUR][1000 genomes]
rs35707555	0.86[EUR][1000 genomes]
rs3885984	0.88[EUR][1000 genomes]
rs3913458	0.98[EUR][1000 genomes]
rs3913459	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4242098	0.87[EUR][1000 genomes]
rs4305644	0.86[EUR][1000 genomes]
rs4320267	0.85[EUR][1000 genomes]
rs4404722	0.95[EUR][1000 genomes]
rs4457090	0.86[EUR][1000 genomes]
rs4460174	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4489104	0.95[EUR][1000 genomes]
rs4533937	0.95[EUR][1000 genomes]
rs4957203	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4957204	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58911119	0.99[EUR][1000 genomes]
rs6451592	0.99[EUR][1000 genomes]
rs6451605	0.80[EUR][1000 genomes]
rs6861819	0.86[EUR][1000 genomes]
rs6872878	0.87[EUR][1000 genomes]
rs6888449	0.88[EUR][1000 genomes]
rs6890248	0.99[EUR][1000 genomes]
rs7713544	0.99[EUR][1000 genomes]
rs7715104	0.95[EUR][1000 genomes]
rs7715374	0.85[EUR][1000 genomes]
rs7718368	0.95[EUR][1000 genomes]
rs905097	1.00[EUR][1000 genomes]
rs905098	0.81[AMR][1000 genomes]
rs9292843	0.99[EUR][1000 genomes]
rs9292848	0.83[EUR][1000 genomes]
rs990898	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1032171	chr5:42015138-42220940	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv462125	chr5:42019110-42192620	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv597885	chr5:42019110-42192620	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1034208	chr5:42119128-42290759	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv969219	chr5:42147728-42169988	ZNF genes & repeats Enhancers Weak transcription Strong transcription	Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv4813	chr5:42157598-42202029	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1501513	ABCA4	trans	parietal	SCAN
rs1501513	OR10V1	trans	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42168200-42168800	Enhancers	H1 Cell Line	embryonic stem cell
2	chr5:42168400-42168800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:42168400-42168800	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr5:42168400-42168800	Enhancers	Esophagus	oesophagus
5	chr5:42168400-42169000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr5:42168400-42169200	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr5:42168600-42169200	Enhancers	HUES48 Cell Line	embryonic stem cell

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