Variant report

Variant	rs6825488
Chromosome Location	chr4:86923847-86923848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10003909	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10305	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1075824	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11097083	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11097084	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11097086	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11097088	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097089	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11547776	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11724577	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12500273	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12503695	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12504340	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12505097	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12507178	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12510562	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12510563	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12650390	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13102197	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13104099	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13110329	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13116843	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13118404	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13121803	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13127513	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13130578	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13137855	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13138054	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13141273	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13142650	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13144829	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13149026	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13149606	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13149705	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1436528	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17011215	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2118042	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2118043	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2164534	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2904086	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35817700	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35832919	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35922412	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3943729	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3943730	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4693133	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4693134	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4693752	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531887	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531888	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66778815	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6813736	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6815772	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6821120	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6825252	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6838333	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6848107	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72660176	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7442034	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7679822	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7686475	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7688039	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs934648	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9685083	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs996804	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9996062	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
rs6825488	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	chr4:86889400-86935000	Weak transcription	Psoas Muscle	Psoas
2	chr4:86899200-86927000	Weak transcription	Lung	lung
3	chr4:86914200-86924000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:86916800-86929400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:86916800-86935800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:86916800-86985400	Weak transcription	Ovary	ovary
7	chr4:86917000-86925000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:86917000-86926000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr4:86917000-86929000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:86917000-86931800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:86917000-86931800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:86917000-86931800	Weak transcription	Osteobl	bone
13	chr4:86917000-86932000	Weak transcription	NHLF	lung
14	chr4:86917000-86932400	Weak transcription	Fetal Lung	lung
15	chr4:86917000-86932400	Weak transcription	Right Ventricle	heart
16	chr4:86917000-86933800	Weak transcription	Gastric	stomach
17	chr4:86917000-86933800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr4:86917000-86935200	Weak transcription	Left Ventricle	heart
19	chr4:86917000-86935800	Weak transcription	Spleen	Spleen
20	chr4:86917000-86954000	Weak transcription	Pancreas	Pancrea
21	chr4:86917200-86932000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:86917400-86924200	Weak transcription	Liver	Liver
23	chr4:86917400-86924600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr4:86917400-86926800	Weak transcription	Fetal Stomach	stomach
25	chr4:86917400-86940400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:86917600-86926000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr4:86917800-86924200	Weak transcription	Fetal Muscle Leg	muscle
28	chr4:86917800-86931600	Weak transcription	NHDF-Ad	bronchial
29	chr4:86918000-86924600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:86918000-86931800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr4:86918200-86924800	Weak transcription	Fetal Kidney	kidney
32	chr4:86919400-86941200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:86919800-86925600	Strong transcription	Primary B cells from peripheral blood	blood
34	chr4:86920200-86933800	Weak transcription	Aorta	Aorta
35	chr4:86920800-86928600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:86921200-86928400	Strong transcription	HUVEC	blood vessel
37	chr4:86921600-86925800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr4:86921800-86932200	Weak transcription	Fetal Heart	heart
39	chr4:86922000-86927200	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr4:86922800-86924600	Weak transcription	HSMMtube	muscle
41	chr4:86922800-86924800	Weak transcription	HSMM	muscle
42	chr4:86922800-86935200	Weak transcription	Right Atrium	heart
43	chr4:86923000-86924400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr4:86923000-86924600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr4:86923200-86924600	Weak transcription	Primary B cells from cord blood	blood
46	chr4:86923400-86931800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:86923600-86924600	Weak transcription	Adipose Nuclei	Adipose

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