Variant report

Variant	rs12774346
Chromosome Location	chr10:51039985-51039986
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	chr10:51038398..51040460-chr10:51042005..51043947,2	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];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	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]
rs17719813	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];1.00[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[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]
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
rs12774346	AGAP6	cis	Nerve Tibial	GTEx
rs12774346	AGAP6	cis	Muscle Skeletal	GTEx
rs12774346	AGAP6	cis	Artery Tibial	GTEx
rs12774346	AGAP6	cis	Esophagus Muscularis	GTEx
rs12774346	AGAP6	cis	Thyroid	GTEx
rs12774346	AGAP6	cis	Esophagus Mucosa	GTEx
rs12774346	AGAP6	cis	Adipose Subcutaneous	GTEx
rs12774346	AGAP6	cis	Whole Blood	GTEx
rs12774346	CTGLF3	cis	multi-tissue	Pritchard
rs12774346	AGAP6	cis	Skin Sun Exposed Lower leg	GTEx
rs12774346	AGAP6	cis	lung	GTEx

Chromatin state (count:125 , 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	chr10:51024000-51052800	Weak transcription	NHLF	lung
4	chr10:51024200-51053200	Weak transcription	Fetal Brain Male	brain
5	chr10:51024600-51054800	Weak transcription	Fetal Heart	heart
6	chr10:51025800-51047800	Weak transcription	HMEC	breast
7	chr10:51026400-51047200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr10:51028200-51046600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr10:51028200-51047000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr10:51028200-51050000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr10:51028200-51053000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr10:51028200-51054600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr10:51028400-51040200	Weak transcription	Right Ventricle	heart
14	chr10:51028400-51049600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr10:51028400-51053000	Weak transcription	Colonic Mucosa	Colon
16	chr10:51028400-51055000	Weak transcription	Spleen	Spleen
17	chr10:51028400-51056200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr10:51028600-51040200	Weak transcription	Brain Anterior Caudate	brain
19	chr10:51028600-51051400	Weak transcription	Fetal Brain Female	brain
20	chr10:51029200-51040000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr10:51030800-51043800	Weak transcription	Fetal Muscle Leg	muscle
22	chr10:51031000-51043200	Weak transcription	A549	lung
23	chr10:51031000-51046800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr10:51031000-51053200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr10:51032600-51042200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr10:51033200-51052000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr10:51033400-51045800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr10:51035000-51043600	Weak transcription	Osteobl	bone
29	chr10:51035800-51043800	Weak transcription	HSMM	muscle
30	chr10:51037000-51040200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr10:51037000-51041200	Strong transcription	Primary B cells from cord blood	blood
32	chr10:51037000-51043800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr10:51037400-51041000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr10:51037400-51042600	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr10:51037600-51040800	Strong transcription	Liver	Liver
36	chr10:51037800-51041000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr10:51037800-51041800	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr10:51038000-51040600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr10:51038000-51041000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr10:51038200-51040200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr10:51038200-51041000	Enhancers	H1 Cell Line	embryonic stem cell
42	chr10:51038200-51052000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr10:51038400-51041000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr10:51038400-51041000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr10:51038800-51040200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr10:51038800-51040600	Strong transcription	Adipose Nuclei	Adipose
47	chr10:51038800-51040600	Strong transcription	Brain Angular Gyrus	brain
48	chr10:51038800-51041000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr10:51038800-51052000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr10:51039000-51040400	Enhancers	Brain Germinal Matrix	brain

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