Variant report

Variant	rs10462034
Chromosome Location	chr5:42307714-42307715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10037143	0.85[EUR][1000 genomes]
rs10050512	0.97[EUR][1000 genomes]
rs10052738	0.88[CEU][hapmap]
rs10054119	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10060873	0.87[EUR][1000 genomes]
rs10064990	0.88[EUR][1000 genomes]
rs10073423	0.97[EUR][1000 genomes]
rs10078494	0.85[EUR][1000 genomes]
rs10078980	0.84[ASN][1000 genomes]
rs10079521	0.88[EUR][1000 genomes]
rs10461734	0.87[EUR][1000 genomes]
rs10461735	0.87[EUR][1000 genomes]
rs10461736	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1073273	0.85[EUR][1000 genomes]
rs1110874	0.86[EUR][1000 genomes]
rs11954853	0.90[EUR][1000 genomes]
rs12153093	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12517869	0.93[ASN][1000 genomes]
rs12519296	1.00[JPT][hapmap]
rs13189999	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1354108	0.88[EUR][1000 genomes]
rs1393017	1.00[JPT][hapmap]
rs1393018	1.00[JPT][hapmap]
rs1501513	0.86[EUR][1000 genomes]
rs1501516	0.87[EUR][1000 genomes]
rs1501517	0.87[EUR][1000 genomes]
rs1501518	0.87[EUR][1000 genomes]
rs1501519	0.87[EUR][1000 genomes]
rs1827329	0.87[EUR][1000 genomes]
rs1827330	0.86[EUR][1000 genomes]
rs1827331	0.87[EUR][1000 genomes]
rs1875430	0.86[EUR][1000 genomes]
rs1876789	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1909951	0.88[EUR][1000 genomes]
rs1995351	0.85[EUR][1000 genomes]
rs2134102	0.85[EUR][1000 genomes]
rs34035285	0.82[EUR][1000 genomes]
rs34813199	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35005365	0.94[EUR][1000 genomes]
rs35707555	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3885984	0.97[EUR][1000 genomes]
rs3913458	0.85[EUR][1000 genomes]
rs3913459	0.84[EUR][1000 genomes]
rs4242098	0.97[EUR][1000 genomes]
rs4305644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4320267	0.99[EUR][1000 genomes]
rs4404722	0.90[EUR][1000 genomes]
rs4457090	0.99[EUR][1000 genomes]
rs4460174	0.90[EUR][1000 genomes]
rs4489104	0.90[EUR][1000 genomes]
rs4533937	0.90[EUR][1000 genomes]
rs4866812	0.86[ASN][1000 genomes]
rs4957203	0.85[EUR][1000 genomes]
rs4957204	0.85[EUR][1000 genomes]
rs58911119	0.85[EUR][1000 genomes]
rs6451592	0.85[EUR][1000 genomes]
rs6451605	0.89[EUR][1000 genomes]
rs6861468	0.80[EUR][1000 genomes]
rs6861819	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872878	0.97[EUR][1000 genomes]
rs6887373	0.90[ASN][1000 genomes]
rs6887391	0.99[ASN][1000 genomes]
rs6887759	0.99[ASN][1000 genomes]
rs6888449	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6890248	0.87[EUR][1000 genomes]
rs73091966	0.81[ASN][1000 genomes]
rs73091974	0.81[ASN][1000 genomes]
rs7380353	0.81[ASN][1000 genomes]
rs7713544	0.85[EUR][1000 genomes]
rs7715104	0.90[EUR][1000 genomes]
rs7715374	0.99[EUR][1000 genomes]
rs7718368	0.90[EUR][1000 genomes]
rs905097	0.86[EUR][1000 genomes]
rs9292843	0.87[EUR][1000 genomes]
rs9292848	0.97[EUR][1000 genomes]
rs9654394	0.81[ASN][1000 genomes]
rs990898	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv880518	chr5:42231896-42375243	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv881090	chr5:42254097-42307714	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv881375	chr5:42254097-42442715	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv948514	chr5:42270161-42519262	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10462034	ABCA4	trans	parietal	SCAN
rs10462034	LIFR	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42307000-42309200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr5:42307200-42309200	Weak transcription	Adipose Nuclei	Adipose

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