Variant report

Variant	rs4957204
Chromosome Location	chr5:42157649-42157650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10037143	1.00[EUR][1000 genomes]
rs10050512	0.87[EUR][1000 genomes]
rs10052738	1.00[CEU][hapmap]
rs10053179	0.87[AFR][1000 genomes]
rs10054119	0.82[EUR][1000 genomes]
rs10060873	0.98[EUR][1000 genomes]
rs10064990	0.97[EUR][1000 genomes]
rs10073423	0.87[EUR][1000 genomes]
rs10078494	1.00[EUR][1000 genomes]
rs10079521	0.97[EUR][1000 genomes]
rs10461734	0.98[EUR][1000 genomes]
rs10461735	0.98[EUR][1000 genomes]
rs10461736	0.87[EUR][1000 genomes]
rs10462034	0.85[EUR][1000 genomes]
rs1073273	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1110874	0.99[EUR][1000 genomes]
rs11954853	0.94[EUR][1000 genomes]
rs12153093	0.87[EUR][1000 genomes]
rs13189999	0.86[EUR][1000 genomes]
rs13436920	1.00[CHD][hapmap]
rs1354108	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1501513	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1501516	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1501517	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1501518	0.98[EUR][1000 genomes]
rs1501519	0.98[EUR][1000 genomes]
rs1827329	0.97[EUR][1000 genomes]
rs1827330	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1827331	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1875430	0.99[EUR][1000 genomes]
rs1909951	0.97[EUR][1000 genomes]
rs1995351	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2134102	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34035285	0.84[EUR][1000 genomes]
rs35005365	0.84[EUR][1000 genomes]
rs35707555	0.85[EUR][1000 genomes]
rs3885984	0.87[EUR][1000 genomes]
rs3913458	0.99[EUR][1000 genomes]
rs3913459	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4242098	0.86[EUR][1000 genomes]
rs4305644	0.85[EUR][1000 genomes]
rs4320267	0.84[EUR][1000 genomes]
rs4404722	0.94[EUR][1000 genomes]
rs4457090	0.85[EUR][1000 genomes]
rs4460174	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4489104	0.94[EUR][1000 genomes]
rs4533937	0.94[EUR][1000 genomes]
rs4957203	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58911119	1.00[EUR][1000 genomes]
rs6451592	1.00[EUR][1000 genomes]
rs6861819	0.85[EUR][1000 genomes]
rs6872878	0.86[EUR][1000 genomes]
rs6888449	0.87[EUR][1000 genomes]
rs6890248	0.98[EUR][1000 genomes]
rs7713544	1.00[EUR][1000 genomes]
rs7715104	0.94[EUR][1000 genomes]
rs7715374	0.84[EUR][1000 genomes]
rs7718368	0.94[EUR][1000 genomes]
rs905097	0.99[EUR][1000 genomes]
rs905098	0.89[AFR][1000 genomes]
rs9292843	0.98[EUR][1000 genomes]
rs9292848	0.82[EUR][1000 genomes]
rs990898	1.00[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
rs4957204	ABCA4	trans	parietal	SCAN
rs4957204	OR10V1	trans	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42152600-42158400	Weak transcription	Adipose Nuclei	Adipose
2	chr5:42153400-42158400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:42157600-42158000	Weak transcription	Fetal Heart	heart

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