Variant report

Variant	rs17719843
Chromosome Location	chr10:51049639-51049640
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10508917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11592062	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11598461	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11599492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11812185	1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11813858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719866	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377698	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2664648	0.85[AFR][1000 genomes]
rs34419748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34714687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35547965	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3877001	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4012652	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4285799	0.81[EUR][1000 genomes]
rs4495813	0.83[EUR][1000 genomes]
rs4592357	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4838566	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4838568	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838573	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4838575	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs5013289	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs61846901	0.80[AMR][1000 genomes]
rs61846915	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61846922	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61846925	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61846931	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7067802	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7089914	0.86[JPT][hapmap]
rs7093312	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7921218	0.82[AFR][1000 genomes];0.83[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
rs17719843	AGAP6	cis	Muscle Skeletal	GTEx
rs17719843	AGAP6	cis	Thyroid	GTEx
rs17719843	AGAP6	cis	Adipose Subcutaneous	GTEx
rs17719843	AGAP6	cis	Artery Tibial	GTEx
rs17719843	CTGLF3	cis	multi-tissue	Pritchard
rs17719843	AGAP6	cis	lung	GTEx
rs17719843	AGAP6	cis	Skin Sun Exposed Lower leg	GTEx
rs17719843	AGAP6	cis	Nerve Tibial	GTEx
rs17719843	AGAP6	cis	Whole Blood	GTEx
rs17719843	AGAP6	cis	Esophagus Mucosa	GTEx
rs17719843	AGAP6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:122 , 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	chr10:51028200-51050000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr10:51028200-51053000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr10:51028200-51054600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr10:51028400-51053000	Weak transcription	Colonic Mucosa	Colon
9	chr10:51028400-51055000	Weak transcription	Spleen	Spleen
10	chr10:51028400-51056200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr10:51028600-51051400	Weak transcription	Fetal Brain Female	brain
12	chr10:51031000-51053200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr10:51033200-51052000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:51038200-51052000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr10:51038800-51052000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr10:51039800-51052800	Weak transcription	NHDF-Ad	bronchial
17	chr10:51040000-51051200	Weak transcription	HSMMtube	muscle
18	chr10:51040000-51051800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr10:51040000-51053400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr10:51040400-51049800	Weak transcription	Brain Germinal Matrix	brain
21	chr10:51040400-51049800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr10:51040400-51050600	Weak transcription	Psoas Muscle	Psoas
23	chr10:51040400-51053200	Weak transcription	Brain Hippocampus Middle	brain
24	chr10:51040400-51053200	Weak transcription	Esophagus	oesophagus
25	chr10:51040600-51049800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr10:51040600-51049800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr10:51040600-51051600	Weak transcription	Right Ventricle	heart
28	chr10:51040600-51052000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:51040600-51053000	Weak transcription	Brain Substantia Nigra	brain
30	chr10:51040600-51053000	Weak transcription	Gastric	stomach
31	chr10:51040600-51053200	Weak transcription	Brain Angular Gyrus	brain
32	chr10:51040600-51053200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr10:51040600-51053400	Weak transcription	Brain Anterior Caudate	brain
34	chr10:51040600-51053400	Weak transcription	Pancreas	Pancrea
35	chr10:51040800-51050000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr10:51040800-51053200	Weak transcription	Colon Smooth Muscle	Colon
37	chr10:51041000-51051600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr10:51041000-51053200	Weak transcription	Aorta	Aorta
39	chr10:51041000-51054000	Weak transcription	Thymus	Thymus
40	chr10:51041000-51055000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr10:51042400-51051800	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr10:51043200-51052000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:51043400-51052000	Strong transcription	Primary B cells from peripheral blood	blood
44	chr10:51043600-51051600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr10:51043600-51051800	Strong transcription	Stomach Smooth Muscle	stomach
46	chr10:51043600-51052000	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr10:51043600-51052200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr10:51043600-51053200	Weak transcription	Stomach Mucosa	stomach
49	chr10:51043800-51052200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr10:51043800-51052200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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