Variant report

Variant	rs10512523
Chromosome Location	chr17:67041060-67041061
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1076401	0.82[ASN][1000 genomes]
rs11077858	0.90[CHB][hapmap]
rs11077859	0.90[CHB][hapmap]
rs11077860	0.90[CHB][hapmap]
rs11453	0.90[CHB][hapmap]
rs11657541	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs11868097	0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs11871766	0.95[CHB][hapmap]
rs11871944	0.95[CHB][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs12325889	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1541470	0.90[CHB][hapmap]
rs16973495	0.90[CHB][hapmap]
rs2079808	0.96[EUR][1000 genomes]
rs2302292	0.90[CHB][hapmap]
rs2302293	0.90[CHB][hapmap]
rs2302294	0.90[CHB][hapmap]
rs4968983	0.90[CHB][hapmap]
rs4968993	0.87[EUR][1000 genomes]
rs62082714	0.81[ASN][1000 genomes]
rs6501944	0.81[CHB][hapmap]
rs6501947	0.90[CHB][hapmap]
rs71357712	0.87[EUR][1000 genomes]
rs7207125	0.95[CHB][hapmap]
rs7215642	0.95[CHB][hapmap]
rs7217543	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs7218871	0.94[CHB][hapmap]
rs8066691	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8066758	0.95[CHB][hapmap]
rs8067578	0.95[EUR][1000 genomes]
rs8068236	0.95[CHB][hapmap]
rs8070285	0.91[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9789039	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9789083	0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs9902602	0.90[EUR][1000 genomes];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	nsv833526	chr17:66980758-67137034	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10512523	ABCA9	cis	parietal	SCAN
rs10512523	ABCA6	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67000200-67044200	Weak transcription	Right Ventricle	heart
2	chr17:67007600-67042200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr17:67008400-67044000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr17:67009200-67043200	Weak transcription	Pancreas	Pancrea
5	chr17:67009400-67044000	Weak transcription	Colon Smooth Muscle	Colon
6	chr17:67010400-67041200	Weak transcription	NHDF-Ad	bronchial
7	chr17:67014000-67044200	Weak transcription	Psoas Muscle	Psoas
8	chr17:67024200-67043200	Weak transcription	Fetal Lung	lung
9	chr17:67035200-67042000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr17:67036600-67042400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr17:67036800-67043200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr17:67038000-67041400	Strong transcription	Liver	Liver
13	chr17:67038000-67041600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr17:67038600-67041400	Strong transcription	Adipose Nuclei	Adipose
15	chr17:67038800-67041200	Weak transcription	K562	blood
16	chr17:67038800-67041400	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr17:67038800-67041600	Weak transcription	HepG2	liver
18	chr17:67038800-67042400	Weak transcription	Stomach Mucosa	stomach
19	chr17:67038800-67043200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr17:67038800-67043200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr17:67039000-67043200	Weak transcription	Small Intestine	intestine
22	chr17:67039400-67043400	Weak transcription	Fetal Stomach	stomach
23	chr17:67039400-67043800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr17:67039600-67041400	Weak transcription	Brain Anterior Caudate	brain
25	chr17:67039600-67042800	Weak transcription	Hela-S3	cervix
26	chr17:67039600-67043200	Weak transcription	Left Ventricle	heart
27	chr17:67039600-67043800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr17:67039600-67044000	Weak transcription	Gastric	stomach
29	chr17:67039800-67041200	Strong transcription	Ovary	ovary
30	chr17:67039800-67042400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr17:67039800-67051800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr17:67040000-67043200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr17:67040000-67044000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr17:67040200-67042400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr17:67040200-67043200	Weak transcription	Fetal Muscle Leg	muscle
36	chr17:67040400-67047600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr17:67040800-67055600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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