Variant report

Variant	rs55671130
Chromosome Location	chr10:51742457-51742458
allele	A/G
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	chr10:51741842-51742485	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RNA5SP317	TF binding region

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

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

rs_ID	r²[population]
rs28595354	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34479769	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35489760	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4935040	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56223978	0.85[EUR][1000 genomes]
rs56411646	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61847131	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61847154	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61848261	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61848272	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71501489	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71502427	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[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
rs55671130	AGAP6	cis	Skin Sun Exposed Lower leg	GTEx
rs55671130	AGAP6	cis	Thyroid	GTEx
rs55671130	AGAP6	cis	Esophagus Muscularis	GTEx
rs55671130	AGAP6	cis	Adipose Subcutaneous	GTEx
rs55671130	AGAP6	cis	Whole Blood	GTEx
rs55671130	AGAP6	cis	lung	GTEx
rs55671130	AGAP6	cis	Nerve Tibial	GTEx
rs55671130	AGAP6	cis	Esophagus Mucosa	GTEx
rs55671130	AGAP6	cis	Artery Tibial	GTEx
rs55671130	AGAP6	cis	Muscle Skeletal	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:51721800-51751800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr10:51721800-51752000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr10:51721800-51752000	Weak transcription	Adipose Nuclei	Adipose
4	chr10:51721800-51777800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr10:51722000-51752200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr10:51722000-51767600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr10:51722200-51752000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:51722400-51743200	Weak transcription	Osteobl	bone
9	chr10:51722400-51743800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr10:51722400-51752200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr10:51722400-51754200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr10:51722400-51770800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr10:51722400-51775800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr10:51722400-51775800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr10:51722400-51777000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr10:51722600-51752200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr10:51722600-51753000	Weak transcription	Fetal Stomach	stomach
18	chr10:51722600-51758600	Weak transcription	Left Ventricle	heart
19	chr10:51722600-51765800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr10:51722600-51770200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr10:51722600-51771200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr10:51722600-51771400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr10:51722800-51757800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr10:51722800-51771200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr10:51723200-51753000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr10:51723400-51772800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr10:51723600-51771000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr10:51724200-51754000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:51724200-51771400	Weak transcription	Fetal Intestine Small	intestine
30	chr10:51724200-51775200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr10:51725600-51754600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr10:51727200-51770400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr10:51727400-51746000	Weak transcription	Dnd41	blood
34	chr10:51727400-51754800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr10:51727400-51770400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr10:51727800-51752200	Weak transcription	Primary T cells from cord blood	blood
37	chr10:51728000-51765800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr10:51728200-51744200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr10:51728200-51754600	Weak transcription	Right Ventricle	heart
40	chr10:51728400-51775800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr10:51728400-51777200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr10:51728800-51752200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr10:51728800-51753000	Weak transcription	Fetal Thymus	thymus
44	chr10:51728800-51769400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr10:51730400-51771000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr10:51730600-51769400	Weak transcription	Fetal Intestine Large	intestine
47	chr10:51731400-51752000	Weak transcription	Liver	Liver
48	chr10:51731600-51757600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr10:51731800-51754600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr10:51732000-51746000	Weak transcription	NHEK	skin

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