Variant report

Variant	rs8474
Chromosome Location	chr10:51026705-51026706
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:51022250..51024471-chr10:51024656..51027577,2	K562	blood:

Variant related genes	Relation type
ENSG00000229870	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10857546	0.81[AMR][1000 genomes]
rs11101238	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1258193	0.81[EUR][1000 genomes]
rs1258194	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1258232	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1438928	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1438929	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1720394	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3793805	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3849145	0.96[EUR][1000 genomes];0.98[ASN][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	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs8474	AGAP6	cis	Adipose Subcutaneous	GTEx
rs8474	AGAP6	cis	Thyroid	GTEx
rs8474	AGAP6	cis	Artery Tibial	GTEx
rs8474	AGAP6	cis	Esophagus Mucosa	GTEx
rs8474	AGAP6	cis	Esophagus Muscularis	GTEx
rs8474	AGAP6	cis	Muscle Skeletal	GTEx
rs8474	AGAP6	cis	Nerve Tibial	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	chr10:51021200-51026800	Weak transcription	Gastric	stomach
4	chr10:51021800-51032800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:51021800-51033400	Weak transcription	Osteobl	bone
6	chr10:51021800-51039600	Weak transcription	Psoas Muscle	Psoas
7	chr10:51022000-51027000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr10:51022000-51027000	Weak transcription	NHEK	skin
9	chr10:51022000-51027200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr10:51022000-51027200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr10:51022000-51027200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr10:51022000-51027200	Weak transcription	Right Ventricle	heart
13	chr10:51022000-51030200	Weak transcription	Fetal Kidney	kidney
14	chr10:51022200-51027000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr10:51022200-51027400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr10:51022200-51034800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr10:51022400-51027000	Weak transcription	Lung	lung
18	chr10:51022600-51035800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr10:51022800-51030000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr10:51023000-51027400	Strong transcription	NHDF-Ad	bronchial
21	chr10:51023000-51028200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr10:51023000-51028200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr10:51023000-51028400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr10:51023000-51028400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr10:51023000-51028400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr10:51023000-51029200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr10:51023000-51030400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:51023000-51031000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr10:51023000-51031000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr10:51023200-51028400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr10:51023200-51029000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr10:51023400-51028600	Strong transcription	Primary B cells from peripheral blood	blood
33	chr10:51023600-51027000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr10:51023600-51028400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr10:51023600-51028600	Strong transcription	A549	lung
36	chr10:51023600-51031000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr10:51023800-51027200	Weak transcription	Spleen	Spleen
38	chr10:51023800-51028000	Weak transcription	Brain Angular Gyrus	brain
39	chr10:51024000-51027000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr10:51024000-51027200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr10:51024000-51028400	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr10:51024000-51036600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr10:51024000-51052800	Weak transcription	NHLF	lung
44	chr10:51024200-51034200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr10:51024200-51053200	Weak transcription	Fetal Brain Male	brain
46	chr10:51024600-51027000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr10:51024600-51030200	Weak transcription	Fetal Lung	lung
48	chr10:51024600-51030400	Strong transcription	HepG2	liver
49	chr10:51024600-51030800	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr10:51024600-51054800	Weak transcription	Fetal Heart	heart

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