Variant report

Variant	rs7089914
Chromosome Location	chr10:51021509-51021510
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:51020009-51022501	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000229870	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs11594575	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11599257	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11812185	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs1258173	1.00[CHB][hapmap]
rs1258180	1.00[CHB][hapmap]
rs1258189	1.00[CHB][hapmap]
rs1258191	0.80[EUR][1000 genomes]
rs12764297	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17719831	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2002273	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4838566	0.86[JPT][hapmap]
rs61846901	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs717721	1.00[CHB][hapmap]

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	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7089914	AGAP6	cis	Nerve Tibial	GTEx
rs7089914	AGAP6	cis	Adipose Subcutaneous	GTEx
rs7089914	AGAP6	cis	Whole Blood	GTEx
rs7089914	AGAP6	cis	Esophagus Mucosa	GTEx
rs7089914	AGAP6	cis	Thyroid	GTEx
rs7089914	CTGLF3	cis	multi-tissue	Pritchard
rs7089914	AGAP6	cis	Artery Tibial	GTEx
rs7089914	AGAP6	cis	Esophagus Muscularis	GTEx
rs7089914	AGAP6	cis	Muscle Skeletal	GTEx
rs7089914	AGAP6	cis	lung	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:51018600-51023200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr10:51019800-51023400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr10:51019800-51053400	Weak transcription	Small Intestine	intestine
4	chr10:51020000-51025200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr10:51020200-51023000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr10:51020400-51049600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr10:51020600-51023000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr10:51020600-51023000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr10:51020800-51022800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr10:51020800-51025400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr10:51021000-51023000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr10:51021000-51023000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr10:51021000-51023000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr10:51021000-51023200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr10:51021200-51023000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr10:51021200-51023000	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr10:51021200-51023000	Weak transcription	Primary B cells from cord blood	blood
18	chr10:51021200-51023000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr10:51021200-51023000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr10:51021200-51023000	Weak transcription	NHDF-Ad	bronchial
21	chr10:51021200-51023200	Weak transcription	Primary T cells from cord blood	blood
22	chr10:51021200-51025400	Weak transcription	Aorta	Aorta
23	chr10:51021200-51025800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr10:51021200-51026800	Weak transcription	Gastric	stomach
25	chr10:51021400-51023000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr10:51021400-51023000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr10:51021400-51023000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr10:51021400-51023000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr10:51021400-51023000	Weak transcription	HSMM	muscle
30	chr10:51021400-51023200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr10:51021400-51023200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr10:51021400-51023200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr10:51021400-51023200	Weak transcription	Brain Germinal Matrix	brain
34	chr10:51021400-51023200	Weak transcription	Placenta	Placenta
35	chr10:51021400-51023200	Weak transcription	Dnd41	blood
36	chr10:51021400-51023200	Weak transcription	NH-A	brain
37	chr10:51021400-51023400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr10:51021400-51025000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr10:51021400-51025200	Weak transcription	Brain Anterior Caudate	brain
40	chr10:51021400-51025400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr10:51021400-51025400	Weak transcription	Brain Hippocampus Middle	brain
42	chr10:51021400-51025600	Weak transcription	GM12878-XiMat	blood

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