Variant report

Variant	rs61848272
Chromosome Location	chr10:51765029-51765030
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs28595354	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34479769	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35489760	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4935040	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55671130	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56223978	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56411646	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs61847131	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61847154	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61848261	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71501489	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71502427	0.86[EUR][1000 genomes];1.00[ASN][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs61848272	AGAP6	cis	Nerve Tibial	GTEx
rs61848272	AGAP6	cis	Skin Sun Exposed Lower leg	GTEx
rs61848272	AGAP6	cis	Artery Tibial	GTEx
rs61848272	AGAP6	cis	Thyroid	GTEx
rs61848272	AGAP6	cis	Esophagus Mucosa	GTEx
rs61848272	AGAP6	cis	Adipose Subcutaneous	GTEx
rs61848272	AGAP6	cis	lung	GTEx
rs61848272	AGAP6	cis	Muscle Skeletal	GTEx
rs61848272	AGAP6	cis	Esophagus Muscularis	GTEx
rs61848272	AGAP6	cis	Whole Blood	GTEx

Chromatin state (count:45 , 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	chr10:51722000-51767600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr10:51722400-51770800	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr10:51722400-51775800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr10:51722400-51775800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr10:51722400-51777000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr10:51722600-51765800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:51722600-51770200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr10:51722600-51771200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr10:51722600-51771400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr10:51722800-51771200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr10:51723400-51772800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr10:51723600-51771000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr10:51724200-51771400	Weak transcription	Fetal Intestine Small	intestine
15	chr10:51724200-51775200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr10:51727200-51770400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr10:51727400-51770400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr10:51728000-51765800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr10:51728400-51775800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr10:51728400-51777200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr10:51728800-51769400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr10:51730400-51771000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr10:51730600-51769400	Weak transcription	Fetal Intestine Large	intestine
24	chr10:51733200-51771000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr10:51734200-51771400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr10:51734400-51775000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr10:51736800-51771000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr10:51738400-51775800	Weak transcription	Lung	lung
29	chr10:51742200-51772000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr10:51746800-51770800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr10:51748000-51770400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr10:51748400-51771800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr10:51752600-51769200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr10:51752600-51772200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr10:51752800-51768600	Weak transcription	Adipose Nuclei	Adipose
36	chr10:51752800-51772400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr10:51753200-51768600	Weak transcription	Liver	Liver
38	chr10:51753200-51775800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr10:51753400-51765200	Weak transcription	Fetal Thymus	thymus
40	chr10:51753400-51768000	Weak transcription	Fetal Stomach	stomach
41	chr10:51753400-51768800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr10:51753400-51769400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr10:51753600-51769200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr10:51759200-51767200	Weak transcription	Left Ventricle	heart
45	chr10:51763400-51771400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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