Variant report

Variant	rs13132564
Chromosome Location	chr4:76883281-76883282
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10008757	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11097189	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11732759	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11931349	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11947509	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13111710	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13125558	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13126007	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13138223	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2242471	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242473	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242474	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292533	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28681066	0.83[ASN][1000 genomes]
rs4282209	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4337760	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859413	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859581	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859582	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859594	0.81[ASN][1000 genomes]
rs6532078	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6826085	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7436021	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7679177	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9307050	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9992952	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9995007	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs13132564	NAAA	cis	Whole Blood	GTEx
rs13132564	ART3	cis	Nerve Tibial	GTEx
rs13132564	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs13132564	NAAA	cis	Adipose Subcutaneous	GTEx
rs13132564	NAAA	cis	Heart Left Ventricle	GTEx
rs13132564	NAAA	cis	Artery Aorta	GTEx
rs13132564	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs13132564	NAAA	cis	Nerve Tibial	GTEx
rs13132564	NAAA	cis	Esophagus Muscularis	GTEx
rs13132564	NAAA	cis	Muscle Skeletal	GTEx
rs13132564	NAAA	cis	Artery Tibial	GTEx
rs13132564	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs13132564	NAAA	cis	lung	GTEx
rs13132564	NAAA	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76862000-76896600	Weak transcription	Stomach Mucosa	stomach
2	chr4:76862200-76886600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:76863000-76903600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:76863800-76884600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:76864600-76884800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:76864800-76883800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:76864800-76884400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:76864800-76884600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:76864800-76903000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:76866400-76886800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:76867400-76885600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:76867400-76886600	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:76867800-76883400	Strong transcription	Fetal Muscle Trunk	muscle
14	chr4:76867800-76884600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:76867800-76888800	Strong transcription	Liver	Liver
16	chr4:76867800-76900000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:76867800-76903800	Strong transcription	Fetal Thymus	thymus
18	chr4:76868000-76884600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:76868000-76884800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:76868000-76886400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:76868000-76886600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:76868000-76899800	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:76868000-76903000	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:76868000-76903000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr4:76868000-76903800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr4:76868200-76903400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:76868200-76903600	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr4:76868400-76903600	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:76868400-76903800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:76868400-76903800	Strong transcription	Placenta	Placenta
31	chr4:76869200-76900200	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr4:76870000-76886800	Strong transcription	Primary T cells from cord blood	blood
33	chr4:76870800-76885600	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr4:76870800-76897600	Strong transcription	Brain Germinal Matrix	brain
35	chr4:76871600-76886600	Strong transcription	Primary B cells from peripheral blood	blood
36	chr4:76872200-76902800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:76873400-76883400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:76873800-76884400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr4:76876200-76884000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr4:76876600-76884800	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:76876600-76886600	Strong transcription	Primary B cells from cord blood	blood
42	chr4:76876800-76895200	Strong transcription	Fetal Kidney	kidney
43	chr4:76879200-76885000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr4:76879600-76884600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr4:76879600-76884800	Weak transcription	Fetal Brain Male	brain
46	chr4:76880000-76886600	Weak transcription	Fetal Heart	heart
47	chr4:76880600-76893400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr4:76881200-76884400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:76881200-76884800	Weak transcription	Brain Angular Gyrus	brain
50	chr4:76881200-76885000	Weak transcription	Hela-S3	cervix

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