Variant report

Variant	rs4838568
Chromosome Location	chr10:51057799-51057800
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10508917	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11592062	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11598461	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11599492	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11812185	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11813858	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774346	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719813	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719843	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719866	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17776131	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377698	0.86[AMR][1000 genomes]
rs2664648	0.81[AFR][1000 genomes]
rs34419748	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34714687	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35547965	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3877001	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4012652	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4285799	0.80[AMR][1000 genomes]
rs4495813	0.81[AMR][1000 genomes]
rs4592357	0.86[AMR][1000 genomes]
rs4838566	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4838573	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4838575	0.90[AMR][1000 genomes]
rs5013289	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs61846901	0.84[AMR][1000 genomes]
rs61846915	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs61846922	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61846925	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61846931	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7067802	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7093312	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7921218	0.82[AMR][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4838568	AGAP6	cis	Adipose Subcutaneous	GTEx
rs4838568	AGAP6	cis	Whole Blood	GTEx
rs4838568	AGAP6	cis	Muscle Skeletal	GTEx
rs4838568	AGAP6	cis	Esophagus Mucosa	GTEx
rs4838568	AGAP6	cis	Skin Sun Exposed Lower leg	GTEx
rs4838568	AGAP6	cis	Esophagus Muscularis	GTEx
rs4838568	AGAP6	cis	Thyroid	GTEx
rs4838568	CTGLF3	cis	multi-tissue	Pritchard
rs4838568	AGAP6	cis	lung	GTEx
rs4838568	AGAP6	cis	Nerve Tibial	GTEx
rs4838568	AGAP6	cis	Artery Tibial	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:51047400-51065600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:51050200-51060000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr10:51050200-51068600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr10:51051600-51067800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr10:51051800-51058000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr10:51051800-51060000	Weak transcription	Left Ventricle	heart
7	chr10:51051800-51068600	Weak transcription	HSMM	muscle
8	chr10:51051800-51102800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr10:51051800-51122000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr10:51052000-51058800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr10:51052000-51062000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr10:51052000-51063200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr10:51052000-51064600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr10:51052000-51093200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr10:51052200-51061600	Weak transcription	Fetal Stomach	stomach
16	chr10:51052200-51062800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr10:51052200-51065200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr10:51052200-51086600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr10:51052200-51094000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr10:51052200-51095000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr10:51053400-51067800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr10:51053400-51086600	Weak transcription	Dnd41	blood
23	chr10:51053400-51090400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr10:51053400-51096400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr10:51053600-51060200	Weak transcription	Osteobl	bone
26	chr10:51053600-51067800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr10:51053600-51070800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr10:51053600-51072400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr10:51053600-51086000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr10:51053600-51092800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:51053600-51093000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr10:51053800-51060200	Weak transcription	Hela-S3	cervix

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