Variant report

Variant	rs3826429
Chromosome Location	chr17:66865466-66865467
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:66851314..66853680-chr17:66863743..66866454,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11652518	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12451146	0.81[ASN][1000 genomes]
rs1373065	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1373067	0.87[MEX][hapmap]
rs1373068	0.87[MEX][hapmap]
rs1443264	0.85[ASN][1000 genomes]
rs16973376	0.89[ASN][1000 genomes]
rs2009065	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2016785	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2053586	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4148005	0.87[MEX][hapmap];0.83[TSI][hapmap]
rs4148009	0.95[ASN][1000 genomes]
rs4148010	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4148012	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4968960	0.81[ASN][1000 genomes]
rs6501832	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6501834	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7216979	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7218530	0.81[ASN][1000 genomes]
rs8071901	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9895870	0.81[ASN][1000 genomes]
rs9896139	0.81[ASN][1000 genomes]
rs9897551	0.81[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
rs3826429	ABCA8	cis	parietal	SCAN
rs3826429	ABCA8	cis	cerebellum	SCAN
rs3826429	LRRC37B	trans	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66858000-66869800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:66858200-66866000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr17:66858200-66869200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr17:66858200-66869200	Weak transcription	Brain Substantia Nigra	brain
5	chr17:66860200-66871200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr17:66861600-66870200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr17:66861800-66869200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr17:66862800-66867800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr17:66863600-66875600	Weak transcription	Fetal Stomach	stomach
10	chr17:66863800-66869200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr17:66864000-66869400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr17:66864400-66866200	Strong transcription	Left Ventricle	heart
13	chr17:66864400-66869200	Weak transcription	Fetal Muscle Leg	muscle
14	chr17:66864400-66869800	Weak transcription	Psoas Muscle	Psoas
15	chr17:66864800-66869200	Strong transcription	Fetal Lung	lung
16	chr17:66865000-66867800	Weak transcription	Small Intestine	intestine
17	chr17:66865000-66869800	Weak transcription	Fetal Brain Male	brain
18	chr17:66865200-66866400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr17:66865200-66867000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:66865200-66869200	Weak transcription	Liver	Liver
21	chr17:66865200-66869400	Weak transcription	Brain Hippocampus Middle	brain
22	chr17:66865400-66865800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr17:66865400-66866200	Weak transcription	Ovary	ovary
24	chr17:66865400-66866600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr17:66865400-66866800	Weak transcription	Adipose Nuclei	Adipose
26	chr17:66865400-66868800	Weak transcription	Fetal Heart	heart
27	chr17:66865400-66871200	Weak transcription	Brain Cingulate Gyrus	brain

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