Variant report

Variant	rs6501834
Chromosome Location	chr17:66869321-66869322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11652518	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1373065	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1373067	0.83[MEX][hapmap]
rs1373068	0.83[MEX][hapmap]
rs1443264	0.82[ASN][1000 genomes]
rs16973376	0.87[ASN][1000 genomes]
rs2009065	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2016785	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053586	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3826429	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]
rs4148005	0.83[MEX][hapmap];0.84[TSI][hapmap]
rs4148009	0.93[ASN][1000 genomes]
rs4148010	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs4148012	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6501832	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7216979	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8071901	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv908695	chr17:66865583-66904001	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6501834	ABCA8	cis	parietal	SCAN
rs6501834	LRRC37B	trans	cerebellum	SCAN
rs6501834	ABCA8	cis	cerebellum	SCAN

Chromatin state (count:35 , 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	chr17:66860200-66871200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:66861600-66870200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr17:66863600-66875600	Weak transcription	Fetal Stomach	stomach
5	chr17:66864000-66869400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr17:66864400-66869800	Weak transcription	Psoas Muscle	Psoas
7	chr17:66865000-66869800	Weak transcription	Fetal Brain Male	brain
8	chr17:66865200-66869400	Weak transcription	Brain Hippocampus Middle	brain
9	chr17:66865400-66871200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr17:66866400-66874200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr17:66866800-66883600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:66867200-66869400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr17:66867200-66874400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr17:66867400-66874000	Weak transcription	Brain Anterior Caudate	brain
15	chr17:66867400-66876200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr17:66867800-66876200	Weak transcription	Osteobl	bone
17	chr17:66868000-66869800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr17:66868200-66869400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr17:66868400-66874200	Weak transcription	Right Ventricle	heart
20	chr17:66868600-66874000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr17:66868800-66870800	Strong transcription	Fetal Heart	heart
22	chr17:66868800-66875800	Strong transcription	Ovary	ovary
23	chr17:66869200-66869400	Strong transcription	Fetal Muscle Leg	muscle
24	chr17:66869200-66869600	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr17:66869200-66869600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
26	chr17:66869200-66869800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr17:66869200-66870200	ZNF genes & repeats	Brain Angular Gyrus	brain
28	chr17:66869200-66870400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr17:66869200-66870400	ZNF genes & repeats	Fetal Lung	lung
30	chr17:66869200-66871800	Strong transcription	Brain Substantia Nigra	brain
31	chr17:66869200-66872000	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr17:66869200-66875800	Strong transcription	Liver	Liver
33	chr17:66869200-66876000	Strong transcription	Adipose Nuclei	Adipose
34	chr17:66869200-66876000	Strong transcription	Left Ventricle	heart
35	chr17:66869200-66903400	Weak transcription	Rectal Smooth Muscle	rectum

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