Variant report

Variant	rs11599492
Chromosome Location	chr10:51032001-51032002
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:51028291..51030720-chr10:51030786..51035251,4	K562	blood:

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];1.00[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];0.82[EUR][1000 genomes]
rs11812185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17776131	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34714687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35547965	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3877001	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4012652	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4495813	0.82[EUR][1000 genomes]
rs4592357	0.82[AMR][1000 genomes]
rs4838566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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];0.83[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];0.81[EUR][1000 genomes]
rs7067802	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7089914	0.86[JPT][hapmap]
rs7093312	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7921218	0.82[AFR][1000 genomes];0.82[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
rs11599492	AGAP6	cis	Muscle Skeletal	GTEx
rs11599492	AGAP6	cis	Esophagus Muscularis	GTEx
rs11599492	AGAP6	cis	Skin Sun Exposed Lower leg	GTEx
rs11599492	AGAP6	cis	Whole Blood	GTEx
rs11599492	AGAP6	cis	Artery Tibial	GTEx
rs11599492	AGAP6	cis	Adipose Subcutaneous	GTEx
rs11599492	AGAP6	cis	Thyroid	GTEx
rs11599492	CTGLF3	cis	multi-tissue	Pritchard
rs11599492	AGAP6	cis	Nerve Tibial	GTEx
rs11599492	AGAP6	cis	Esophagus Mucosa	GTEx
rs11599492	AGAP6	cis	lung	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	chr10:51020400-51049600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr10:51021800-51032800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:51021800-51033400	Weak transcription	Osteobl	bone
5	chr10:51021800-51039600	Weak transcription	Psoas Muscle	Psoas
6	chr10:51022200-51034800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr10:51022600-51035800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr10:51024000-51036600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr10:51024000-51052800	Weak transcription	NHLF	lung
10	chr10:51024200-51034200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr10:51024200-51053200	Weak transcription	Fetal Brain Male	brain
12	chr10:51024600-51054800	Weak transcription	Fetal Heart	heart
13	chr10:51025800-51037000	Strong transcription	Primary T cells from cord blood	blood
14	chr10:51025800-51047800	Weak transcription	HMEC	breast
15	chr10:51026200-51039000	Weak transcription	Colon Smooth Muscle	Colon
16	chr10:51026200-51039600	Weak transcription	Brain Hippocampus Middle	brain
17	chr10:51026400-51047200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr10:51027200-51038000	Weak transcription	HUVEC	blood vessel
19	chr10:51027600-51034400	Weak transcription	HSMMtube	muscle
20	chr10:51027600-51034800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr10:51027800-51039400	Weak transcription	Esophagus	oesophagus
22	chr10:51028000-51039400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr10:51028000-51039600	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr10:51028200-51032800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr10:51028200-51034000	Weak transcription	Fetal Thymus	thymus
26	chr10:51028200-51034200	Weak transcription	Brain Angular Gyrus	brain
27	chr10:51028200-51034800	Weak transcription	Fetal Intestine Large	intestine
28	chr10:51028200-51036400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr10:51028200-51039600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr10:51028200-51039600	Weak transcription	Brain Substantia Nigra	brain
31	chr10:51028200-51039600	Weak transcription	Lung	lung
32	chr10:51028200-51046600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr10:51028200-51047000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr10:51028200-51050000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr10:51028200-51053000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr10:51028200-51054600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr10:51028400-51033200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr10:51028400-51033400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr10:51028400-51034200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr10:51028400-51034200	Weak transcription	NH-A	brain
41	chr10:51028400-51034400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr10:51028400-51034400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr10:51028400-51035000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr10:51028400-51035200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr10:51028400-51035600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr10:51028400-51036200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr10:51028400-51039000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr10:51028400-51039400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr10:51028400-51039600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr10:51028400-51039600	Weak transcription	Brain Inferior Temporal Lobe	brain

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