Variant report

Variant	rs17719866
Chromosome Location	chr10:51051329-51051330
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10508917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11592062	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11598461	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11599492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11812185	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11813858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12774346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17719813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17719843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17776131	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2377698	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2664648	0.85[AFR][1000 genomes]
rs34419748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34714687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35547965	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3877001	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4012652	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4285799	0.83[EUR][1000 genomes]
rs4495813	0.85[EUR][1000 genomes]
rs4592357	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4838566	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4838568	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4838573	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4838575	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5013289	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61846901	0.80[AMR][1000 genomes]
rs61846915	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61846922	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61846925	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61846931	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7067802	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7093312	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7921218	0.82[AFR][1000 genomes];0.85[EUR][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	esv2758219	chr10:50971974-51925166	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	esv2759749	chr10:50971974-51925166	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv428232	chr10:50971974-51925166	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv895379	chr10:51022933-51187793	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs17719866	AGAP6	cis	Whole Blood	GTEx
rs17719866	AGAP6	cis	Adipose Subcutaneous	GTEx
rs17719866	AGAP6	cis	Nerve Tibial	GTEx
rs17719866	AGAP6	cis	Esophagus Muscularis	GTEx
rs17719866	AGAP6	cis	Thyroid	GTEx
rs17719866	AGAP6	cis	Artery Tibial	GTEx
rs17719866	CTGLF3	cis	multi-tissue	Pritchard
rs17719866	AGAP6	cis	Esophagus Mucosa	GTEx
rs17719866	AGAP6	cis	Muscle Skeletal	GTEx
rs17719866	AGAP6	cis	Skin Sun Exposed Lower leg	GTEx
rs17719866	AGAP6	cis	lung	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:51019800-51053400	Weak transcription	Small Intestine	intestine
2	chr10:51024000-51052800	Weak transcription	NHLF	lung
3	chr10:51024200-51053200	Weak transcription	Fetal Brain Male	brain
4	chr10:51024600-51054800	Weak transcription	Fetal Heart	heart
5	chr10:51028200-51053000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr10:51028200-51054600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr10:51028400-51053000	Weak transcription	Colonic Mucosa	Colon
8	chr10:51028400-51055000	Weak transcription	Spleen	Spleen
9	chr10:51028400-51056200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr10:51028600-51051400	Weak transcription	Fetal Brain Female	brain
11	chr10:51031000-51053200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr10:51033200-51052000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:51038200-51052000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr10:51038800-51052000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr10:51039800-51052800	Weak transcription	NHDF-Ad	bronchial
16	chr10:51040000-51051800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr10:51040000-51053400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr10:51040400-51053200	Weak transcription	Brain Hippocampus Middle	brain
19	chr10:51040400-51053200	Weak transcription	Esophagus	oesophagus
20	chr10:51040600-51051600	Weak transcription	Right Ventricle	heart
21	chr10:51040600-51052000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr10:51040600-51053000	Weak transcription	Brain Substantia Nigra	brain
23	chr10:51040600-51053000	Weak transcription	Gastric	stomach
24	chr10:51040600-51053200	Weak transcription	Brain Angular Gyrus	brain
25	chr10:51040600-51053200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr10:51040600-51053400	Weak transcription	Brain Anterior Caudate	brain
27	chr10:51040600-51053400	Weak transcription	Pancreas	Pancrea
28	chr10:51040800-51053200	Weak transcription	Colon Smooth Muscle	Colon
29	chr10:51041000-51051600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr10:51041000-51053200	Weak transcription	Aorta	Aorta
31	chr10:51041000-51054000	Weak transcription	Thymus	Thymus
32	chr10:51041000-51055000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr10:51042400-51051800	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr10:51043200-51052000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr10:51043400-51052000	Strong transcription	Primary B cells from peripheral blood	blood
36	chr10:51043600-51051600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr10:51043600-51051800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr10:51043600-51052000	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr10:51043600-51052200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr10:51043600-51053200	Weak transcription	Stomach Mucosa	stomach
41	chr10:51043800-51052200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr10:51043800-51052200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr10:51044200-51052800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr10:51044400-51053600	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr10:51044600-51051800	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr10:51044800-51051800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr10:51044800-51052200	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr10:51045000-51052000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr10:51045000-51053600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr10:51045200-51052000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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