Variant report

Variant	rs1258232
Chromosome Location	chr10:51021095-51021096
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10857546	0.82[AMR][1000 genomes]
rs11101238	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1258193	0.82[EUR][1000 genomes]
rs1258194	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1438928	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1438929	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1720394	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3793805	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3849145	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8474	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1258232	AGAP6	cis	Thyroid	GTEx
rs1258232	AGAP6	cis	Nerve Tibial	GTEx
rs1258232	AGAP6	cis	Adipose Subcutaneous	GTEx
rs1258232	AGAP6	cis	Artery Tibial	GTEx
rs1258232	AGAP6	cis	Muscle Skeletal	GTEx
rs1258232	AGAP6	cis	Esophagus Muscularis	GTEx
rs1258232	AGAP6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:17 , 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	chr10:51021000-51021200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr10:51021000-51021200	ZNF genes & repeats	Aorta	Aorta
13	chr10:51021000-51021200	ZNF genes & repeats	Gastric	stomach
14	chr10:51021000-51023000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr10:51021000-51023000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr10:51021000-51023000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr10:51021000-51023200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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