Variant report

Variant	rs4367907
Chromosome Location	chr10:46088557-46088558
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11239562	0.81[AMR][1000 genomes]
rs3802542	0.94[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs4948674	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4949013	0.94[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs7081687	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430166	chr10:45668894-46148794	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv993428	chr10:45742877-46224333	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv895108	chr10:45878908-46224333	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv895109	chr10:45882741-46210665	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv895112	chr10:46012620-46202216	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	esv2761592	chr10:46072872-46090202	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4367907	AGAP4	cis	Muscle Skeletal	GTEx
rs4367907	AGAP4	cis	Artery Tibial	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:46076800-46089000	Weak transcription	Right Ventricle	heart
2	chr10:46080400-46088800	Weak transcription	A549	lung
3	chr10:46081600-46089000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr10:46083400-46088800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr10:46083400-46088800	Weak transcription	Aorta	Aorta
6	chr10:46084000-46088800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr10:46084000-46088800	Weak transcription	Fetal Intestine Small	intestine
8	chr10:46084400-46088800	Weak transcription	Fetal Stomach	stomach
9	chr10:46084800-46088600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:46085400-46089400	Weak transcription	Placenta	Placenta
11	chr10:46085800-46088800	Weak transcription	Fetal Kidney	kidney
12	chr10:46086000-46088600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr10:46086000-46088800	Weak transcription	HSMMtube	muscle
14	chr10:46086000-46089000	Weak transcription	Fetal Muscle Leg	muscle
15	chr10:46086000-46089200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr10:46086200-46089000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr10:46086400-46089000	Weak transcription	Pancreas	Pancrea
18	chr10:46086800-46088600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr10:46086800-46089800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:46087000-46089000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr10:46087000-46089000	Weak transcription	Left Ventricle	heart
22	chr10:46087000-46089600	Weak transcription	Esophagus	oesophagus
23	chr10:46087000-46090800	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr10:46087200-46088600	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr10:46087200-46088600	Enhancers	Liver	Liver
26	chr10:46087200-46088600	Enhancers	HepG2	liver
27	chr10:46087200-46088800	Enhancers	Primary B cells from peripheral blood	blood
28	chr10:46087200-46088800	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr10:46087200-46088800	Active TSS	GM12878-XiMat	blood
30	chr10:46087200-46089000	Weak transcription	Stomach Mucosa	stomach
31	chr10:46087400-46088800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr10:46087400-46089000	Weak transcription	Small Intestine	intestine
33	chr10:46087400-46089200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr10:46087600-46088600	Weak transcription	Brain Germinal Matrix	brain
35	chr10:46087600-46088800	Enhancers	Brain Hippocampus Middle	brain
36	chr10:46087600-46090000	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr10:46087800-46088600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr10:46087800-46088600	Enhancers	Colon Smooth Muscle	Colon
39	chr10:46087800-46088800	Enhancers	Brain Substantia Nigra	brain
40	chr10:46087800-46089400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr10:46087800-46089600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr10:46088000-46088600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr10:46088000-46088600	Enhancers	Brain Anterior Caudate	brain
44	chr10:46088000-46088600	Active TSS	Fetal Brain Male	brain
45	chr10:46088000-46088600	Enhancers	Hela-S3	cervix
46	chr10:46088000-46088600	Enhancers	HMEC	breast
47	chr10:46088000-46088600	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr10:46088000-46089200	Enhancers	Primary T cells fromperipheralblood	blood
49	chr10:46088000-46089400	Active TSS	Colonic Mucosa	Colon
50	chr10:46088000-46089600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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