Variant report

Variant	rs4012652
Chromosome Location	chr10:51118419-51118420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10508917	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11592062	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11598461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11598949	0.80[AFR][1000 genomes]
rs11599492	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11812185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11813858	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12774346	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17719813	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17719843	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17719866	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17776131	0.81[EUR][1000 genomes]
rs2377698	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34419748	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34714687	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs35547965	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3877001	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4285799	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4495813	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4592357	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4838568	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4838573	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838575	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5013289	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61846915	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs61846922	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61846925	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61846931	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7067802	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7089914	0.86[JPT][hapmap]
rs7093312	0.82[EUR][1000 genomes]
rs7921218	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	esv32940	chr10:51051718-51488059	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv895381	chr10:51094660-51515534	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4012652	AGAP6	cis	Adipose Subcutaneous	GTEx
rs4012652	AGAP6	cis	Skin Sun Exposed Lower leg	GTEx
rs4012652	AGAP6	cis	Artery Tibial	GTEx
rs4012652	AGAP6	cis	Esophagus Muscularis	GTEx
rs4012652	AGAP6	cis	Esophagus Mucosa	GTEx
rs4012652	AGAP6	cis	Whole Blood	GTEx
rs4012652	AGAP6	cis	lung	GTEx
rs4012652	AGAP6	cis	Muscle Skeletal	GTEx
rs4012652	AGAP6	cis	Nerve Tibial	GTEx
rs4012652	AGAP6	cis	Thyroid	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:51051800-51122000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr10:51080800-51130200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:51084400-51131800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr10:51084600-51130200	Weak transcription	Fetal Lung	lung
5	chr10:51084600-51136000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr10:51084600-51136600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr10:51084600-51137800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr10:51085000-51127200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr10:51085400-51138200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr10:51085400-51138600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr10:51087000-51132000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr10:51087600-51122000	Weak transcription	Primary B cells from cord blood	blood
13	chr10:51087600-51122400	Weak transcription	Adipose Nuclei	Adipose
14	chr10:51089800-51120600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr10:51089800-51121800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr10:51091200-51138000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr10:51095000-51137200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr10:51098200-51122000	Weak transcription	K562	blood
19	chr10:51100800-51137600	Weak transcription	Lung	lung
20	chr10:51101200-51119800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr10:51102000-51138000	Weak transcription	Spleen	Spleen
22	chr10:51102600-51122000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr10:51103200-51127800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr10:51103800-51119600	Weak transcription	Fetal Stomach	stomach
25	chr10:51103800-51138000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr10:51104400-51121000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr10:51104400-51122200	Weak transcription	Dnd41	blood
28	chr10:51104600-51120200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:51104600-51125200	Weak transcription	Liver	Liver
30	chr10:51104600-51127800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr10:51108200-51122000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr10:51108400-51120200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr10:51108600-51129600	Weak transcription	HSMMtube	muscle
34	chr10:51108800-51120800	Weak transcription	NHEK	skin
35	chr10:51108800-51137400	Weak transcription	Ovary	ovary
36	chr10:51109000-51138200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr10:51109200-51120400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr10:51109600-51119800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr10:51109600-51120200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr10:51109600-51120400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr10:51109800-51120400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr10:51110000-51137600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr10:51110200-51120400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr10:51110200-51121800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr10:51110400-51137400	Weak transcription	Thymus	Thymus
46	chr10:51110800-51122000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr10:51111000-51122200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr10:51111000-51122200	Weak transcription	Hela-S3	cervix
49	chr10:51111200-51120600	Weak transcription	Primary T cells from cord blood	blood
50	chr10:51111200-51136200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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