Variant report

Variant	rs13130578
Chromosome Location	chr4:86903514-86903515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10003909	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10305	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1075824	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11097083	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11097084	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097086	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097088	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097089	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11547776	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11724577	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12500273	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12503695	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12504340	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12505097	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12507178	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12510562	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12510563	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12650390	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13102197	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13104099	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13110329	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13116843	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13118404	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13121803	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13127513	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13137855	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13138054	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13141273	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13142650	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13144829	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13149026	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13149606	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13149705	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1436528	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17011215	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2118042	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2118043	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2164534	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2904086	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35817700	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35832919	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35922412	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3943729	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3943730	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4693133	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4693134	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4693752	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6531887	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6531888	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66778815	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6813736	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6815772	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6821120	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6825252	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6825488	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6838333	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6848107	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72660176	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7442034	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7679822	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7686475	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7688039	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs934648	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9685083	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs996804	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9996062	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830000	chr4:86745341-86909059	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv879520	chr4:86829529-86918232	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1009622	chr4:86893536-87119153	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1005257	chr4:86899596-86925469	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13130578	RP11-778J15.1	cis	Artery Tibial	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86854200-86915800	Weak transcription	Left Ventricle	heart
2	chr4:86875200-86915800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:86880600-86915800	Weak transcription	Gastric	stomach
4	chr4:86885000-86915600	Weak transcription	Fetal Lung	lung
5	chr4:86887600-86915600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:86888800-86919200	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:86889400-86915800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:86889400-86935000	Weak transcription	Psoas Muscle	Psoas
9	chr4:86889600-86904000	Weak transcription	Aorta	Aorta
10	chr4:86890400-86916000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:86891400-86915800	Weak transcription	HSMMtube	muscle
12	chr4:86891800-86905400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:86892000-86904000	Weak transcription	Adipose Nuclei	Adipose
14	chr4:86892000-86915600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:86892000-86915600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:86892000-86915800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:86892000-86916000	Weak transcription	Spleen	Spleen
18	chr4:86893000-86906600	Strong transcription	HUVEC	blood vessel
19	chr4:86893200-86906600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:86893200-86908600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr4:86894000-86907400	Weak transcription	Osteobl	bone
22	chr4:86894400-86915800	Weak transcription	Ovary	ovary
23	chr4:86895000-86910400	Strong transcription	Primary B cells from cord blood	blood
24	chr4:86895400-86903800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:86897000-86906800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:86897600-86915600	Weak transcription	Placenta	Placenta
27	chr4:86897600-86916000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr4:86897600-86916400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:86897800-86906800	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr4:86899200-86927000	Weak transcription	Lung	lung
31	chr4:86899800-86915800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr4:86899800-86915800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr4:86899800-86917800	Weak transcription	Small Intestine	intestine
34	chr4:86900000-86915600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr4:86900000-86915800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr4:86900200-86915800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:86901000-86915800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr4:86901400-86905000	Strong transcription	Fetal Kidney	kidney
39	chr4:86901600-86915800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:86901800-86904200	Strong transcription	Fetal Muscle Trunk	muscle
41	chr4:86901800-86906000	Strong transcription	Fetal Muscle Leg	muscle
42	chr4:86902200-86915800	Weak transcription	Pancreas	Pancrea
43	chr4:86902400-86905600	Strong transcription	HSMM	muscle
44	chr4:86902600-86904200	Strong transcription	Fetal Stomach	stomach
45	chr4:86902800-86915800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:86902800-86915800	Weak transcription	Liver	Liver
47	chr4:86903000-86914600	Weak transcription	NHDF-Ad	bronchial

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