Variant report

Variant	rs17719813
Chromosome Location	chr10:51039436-51039437
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:51038398..51040460-chr10:51042005..51043947,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:32)

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];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11598461	0.90[AFR][1000 genomes];0.81[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	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11813858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719843	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];0.96[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]
rs2664648	0.85[AFR][1000 genomes]
rs34419748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34714687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35547965	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3877001	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4012652	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4495813	0.81[EUR][1000 genomes]
rs4592357	0.82[AMR][1000 genomes]
rs4838566	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4838568	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838573	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4838575	0.86[AMR][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];0.82[EUR][1000 genomes]
rs61846922	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61846925	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61846931	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7067802	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7093312	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7921218	0.82[AFR][1000 genomes];0.81[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
rs17719813	AGAP6	cis	lung	GTEx
rs17719813	AGAP6	cis	Muscle Skeletal	GTEx
rs17719813	CTGLF3	cis	multi-tissue	Pritchard
rs17719813	AGAP6	cis	Adipose Subcutaneous	GTEx
rs17719813	AGAP6	cis	Artery Tibial	GTEx
rs17719813	AGAP6	cis	Esophagus Muscularis	GTEx
rs17719813	AGAP6	cis	Whole Blood	GTEx
rs17719813	AGAP6	cis	Nerve Tibial	GTEx
rs17719813	AGAP6	cis	Thyroid	GTEx
rs17719813	AGAP6	cis	Esophagus Mucosa	GTEx
rs17719813	AGAP6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:123 , 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	chr10:51020400-51049600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr10:51021800-51039600	Weak transcription	Psoas Muscle	Psoas
4	chr10:51024000-51052800	Weak transcription	NHLF	lung
5	chr10:51024200-51053200	Weak transcription	Fetal Brain Male	brain
6	chr10:51024600-51054800	Weak transcription	Fetal Heart	heart
7	chr10:51025800-51047800	Weak transcription	HMEC	breast
8	chr10:51026200-51039600	Weak transcription	Brain Hippocampus Middle	brain
9	chr10:51026400-51047200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr10:51028000-51039600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr10:51028200-51039600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr10:51028200-51039600	Weak transcription	Brain Substantia Nigra	brain
13	chr10:51028200-51039600	Weak transcription	Lung	lung
14	chr10:51028200-51046600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr10:51028200-51047000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr10:51028200-51050000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr10:51028200-51053000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr10:51028200-51054600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr10:51028400-51039600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr10:51028400-51039600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr10:51028400-51039600	Weak transcription	Gastric	stomach
22	chr10:51028400-51039600	Weak transcription	K562	blood
23	chr10:51028400-51040200	Weak transcription	Right Ventricle	heart
24	chr10:51028400-51049600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr10:51028400-51053000	Weak transcription	Colonic Mucosa	Colon
26	chr10:51028400-51055000	Weak transcription	Spleen	Spleen
27	chr10:51028400-51056200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr10:51028600-51039600	Weak transcription	Pancreas	Pancrea
29	chr10:51028600-51039600	Weak transcription	Thymus	Thymus
30	chr10:51028600-51040200	Weak transcription	Brain Anterior Caudate	brain
31	chr10:51028600-51051400	Weak transcription	Fetal Brain Female	brain
32	chr10:51029200-51040000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr10:51030600-51039600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr10:51030800-51043800	Weak transcription	Fetal Muscle Leg	muscle
35	chr10:51031000-51043200	Weak transcription	A549	lung
36	chr10:51031000-51046800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr10:51031000-51053200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr10:51032600-51042200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr10:51033200-51052000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:51033400-51045800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr10:51035000-51043600	Weak transcription	Osteobl	bone
42	chr10:51035200-51039600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr10:51035200-51039600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr10:51035200-51039600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr10:51035400-51039600	Weak transcription	Fetal Lung	lung
46	chr10:51035600-51039600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr10:51035600-51039800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr10:51035800-51039600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr10:51035800-51043800	Weak transcription	HSMM	muscle
50	chr10:51036000-51039600	Weak transcription	Muscle Satellite Cultured Cells	--

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