Variant report

Variant	rs56223978
Chromosome Location	chr10:51777325-51777326
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs28595354	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34479769	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35489760	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4935040	0.84[EUR][1000 genomes]
rs55671130	0.85[EUR][1000 genomes]
rs56411646	0.82[AMR][1000 genomes]
rs61847131	0.82[AMR][1000 genomes]
rs61847154	0.83[EUR][1000 genomes]
rs61848261	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs61848272	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71501489	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71502427	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv1830900	chr10:51187411-51903662	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	esv1815597	chr10:51525699-51804254	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv518071	chr10:51595893-52157935	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	esv3521278	chr10:51635096-52001994	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	esv3521279	chr10:51635096-52001994	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs56223978	AGAP6	cis	lung	GTEx
rs56223978	AGAP6	cis	Esophagus Muscularis	GTEx
rs56223978	AGAP6	cis	Nerve Tibial	GTEx
rs56223978	AGAP6	cis	Artery Tibial	GTEx
rs56223978	AGAP6	cis	Esophagus Mucosa	GTEx
rs56223978	AGAP6	cis	Adipose Subcutaneous	GTEx
rs56223978	AGAP6	cis	Muscle Skeletal	GTEx
rs56223978	AGAP6	cis	Whole Blood	GTEx
rs56223978	AGAP6	cis	Thyroid	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:51721800-51777800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr10:51776200-51777400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr10:51776200-51777600	Weak transcription	Osteobl	bone
4	chr10:51776200-51778200	Weak transcription	Adipose Nuclei	Adipose
5	chr10:51776200-51778200	Weak transcription	Right Atrium	heart
6	chr10:51776200-51781400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:51776200-51784600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr10:51777000-51778400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr10:51777200-51778000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr10:51777200-51778400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr10:51777200-51779200	Enhancers	Pancreas	Pancrea

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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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