Variant report

Variant	rs11652518
Chromosome Location	chr17:66862176-66862177
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1373065	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1373067	0.83[MEX][hapmap]
rs1373068	0.83[MEX][hapmap]
rs16973376	1.00[ASN][1000 genomes]
rs2009065	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2016785	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2053586	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3826429	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4148005	0.83[MEX][hapmap];0.83[TSI][hapmap]
rs4148009	0.85[ASN][1000 genomes]
rs4148010	1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs4148012	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6501832	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6501834	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7216979	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8071901	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][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	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv908694	chr17:66802992-66913936	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11652518	ABCA8	cis	cerebellum	SCAN
rs11652518	ABCA8	cis	parietal	SCAN
rs11652518	LRRC37B	trans	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66850400-66864000	Weak transcription	Ovary	ovary
2	chr17:66858000-66869800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:66858200-66864800	Weak transcription	Adipose Nuclei	Adipose
4	chr17:66858200-66866000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr17:66858200-66869200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr17:66858200-66869200	Weak transcription	Brain Substantia Nigra	brain
7	chr17:66858400-66864600	Weak transcription	Liver	Liver
8	chr17:66858600-66863600	Weak transcription	Fetal Heart	heart
9	chr17:66858800-66864800	Weak transcription	Fetal Lung	lung
10	chr17:66860200-66864600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr17:66860200-66871200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr17:66860400-66862800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr17:66861600-66870200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr17:66861800-66869200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr17:66862000-66862200	ZNF genes & repeats	Psoas Muscle	Psoas

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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