Variant report

Variant	rs2664648
Chromosome Location	chr10:51053834-51053835
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10508917	0.85[AFR][1000 genomes]
rs11592062	0.85[AFR][1000 genomes]
rs11599492	0.85[AFR][1000 genomes]
rs11813858	0.85[AFR][1000 genomes]
rs12774346	0.85[AFR][1000 genomes]
rs17719813	0.85[AFR][1000 genomes]
rs17719843	0.85[AFR][1000 genomes]
rs17719866	0.85[AFR][1000 genomes]
rs34419748	0.85[AFR][1000 genomes]
rs34714687	0.85[AFR][1000 genomes]
rs35547965	0.85[AFR][1000 genomes]
rs4838566	0.85[AFR][1000 genomes]
rs4838568	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2664648	AGAP6	cis	lung	GTEx
rs2664648	AGAP6	cis	Thyroid	GTEx
rs2664648	AGAP6	cis	Esophagus Mucosa	GTEx
rs2664648	AGAP6	cis	Adipose Subcutaneous	GTEx
rs2664648	AGAP6	cis	Artery Tibial	GTEx
rs2664648	AGAP6	cis	Esophagus Muscularis	GTEx
rs2664648	AGAP6	cis	Nerve Tibial	GTEx
rs2664648	AGAP6	cis	Whole Blood	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:51024600-51054800	Weak transcription	Fetal Heart	heart
2	chr10:51028200-51054600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr10:51028400-51055000	Weak transcription	Spleen	Spleen
4	chr10:51028400-51056200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr10:51041000-51054000	Weak transcription	Thymus	Thymus
6	chr10:51041000-51055000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr10:51047200-51055000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr10:51047400-51065600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr10:51048400-51054800	Weak transcription	Primary B cells from cord blood	blood
10	chr10:51050200-51054600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr10:51050200-51060000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr10:51050200-51068600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr10:51050400-51056200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr10:51050800-51055000	Weak transcription	GM12878-XiMat	blood
15	chr10:51051600-51054800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr10:51051600-51067800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr10:51051800-51055000	Weak transcription	K562	blood
18	chr10:51051800-51057000	Weak transcription	HSMMtube	muscle
19	chr10:51051800-51057200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr10:51051800-51058000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr10:51051800-51060000	Weak transcription	Left Ventricle	heart
22	chr10:51051800-51068600	Weak transcription	HSMM	muscle
23	chr10:51051800-51102800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr10:51051800-51122000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr10:51052000-51054200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr10:51052000-51054400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr10:51052000-51054400	Weak transcription	Primary T cells from cord blood	blood
28	chr10:51052000-51054600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr10:51052000-51055000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr10:51052000-51055200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr10:51052000-51056200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr10:51052000-51058800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr10:51052000-51062000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr10:51052000-51063200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr10:51052000-51064600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr10:51052000-51093200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr10:51052200-51054800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr10:51052200-51055000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr10:51052200-51056600	Weak transcription	Ovary	ovary
40	chr10:51052200-51061600	Weak transcription	Fetal Stomach	stomach
41	chr10:51052200-51062800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr10:51052200-51065200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr10:51052200-51086600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr10:51052200-51094000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr10:51052200-51095000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr10:51052600-51054600	Weak transcription	Fetal Muscle Leg	muscle
47	chr10:51053400-51067800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr10:51053400-51086600	Weak transcription	Dnd41	blood
49	chr10:51053400-51090400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr10:51053400-51096400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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