Variant report

Variant	rs12505097
Chromosome Location	chr4:86921612-86921613
allele	C/G
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	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10305	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1075824	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11097083	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11097084	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11097086	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11097088	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11097089	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11547776	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11724577	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12500273	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12503695	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12504340	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12507178	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12510562	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12510563	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12650390	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13102197	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13104099	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13110329	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13116843	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13118404	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13121803	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13127513	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13130578	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13137855	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13138054	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13141273	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13142650	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13144829	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13149026	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13149606	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13149705	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1436528	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17011215	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2118042	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2118043	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2164534	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2904086	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35817700	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35832919	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35922412	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3943729	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3943730	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4693133	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4693134	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4693752	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531887	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531888	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66778815	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6813736	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6815772	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6821120	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6825252	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6825488	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6838333	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6848107	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72660176	0.81[EUR][1000 genomes]
rs7442034	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7679822	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7686475	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7688039	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs934648	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9685083	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs996804	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9996062	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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
rs12505097	RP11-778J15.1	cis	Artery Tibial	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

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	chr4:86914800-86923200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:86916600-86923600	Weak transcription	Fetal Intestine Small	intestine
6	chr4:86916800-86923200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:86916800-86923200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:86916800-86929400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:86916800-86935800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:86916800-86985400	Weak transcription	Ovary	ovary
11	chr4:86917000-86923400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:86917000-86925000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:86917000-86926000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:86917000-86929000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:86917000-86931800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:86917000-86931800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:86917000-86931800	Weak transcription	Osteobl	bone
18	chr4:86917000-86932000	Weak transcription	NHLF	lung
19	chr4:86917000-86932400	Weak transcription	Fetal Lung	lung
20	chr4:86917000-86932400	Weak transcription	Right Ventricle	heart
21	chr4:86917000-86933800	Weak transcription	Gastric	stomach
22	chr4:86917000-86933800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr4:86917000-86935200	Weak transcription	Left Ventricle	heart
24	chr4:86917000-86935800	Weak transcription	Spleen	Spleen
25	chr4:86917000-86954000	Weak transcription	Pancreas	Pancrea
26	chr4:86917200-86921800	Weak transcription	HSMMtube	muscle
27	chr4:86917200-86932000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:86917400-86924200	Weak transcription	Liver	Liver
29	chr4:86917400-86924600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:86917400-86926800	Weak transcription	Fetal Stomach	stomach
31	chr4:86917400-86940400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr4:86917600-86922600	Weak transcription	HSMM	muscle
33	chr4:86917600-86926000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:86917800-86924200	Weak transcription	Fetal Muscle Leg	muscle
35	chr4:86917800-86931600	Weak transcription	NHDF-Ad	bronchial
36	chr4:86918000-86924600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:86918000-86931800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr4:86918200-86922000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:86918200-86924800	Weak transcription	Fetal Kidney	kidney
40	chr4:86919400-86941200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:86919800-86925600	Strong transcription	Primary B cells from peripheral blood	blood
42	chr4:86920200-86933800	Weak transcription	Aorta	Aorta
43	chr4:86920800-86922000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr4:86920800-86928600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:86921200-86928400	Strong transcription	HUVEC	blood vessel
46	chr4:86921400-86921800	Enhancers	Fetal Heart	heart
47	chr4:86921400-86922000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr4:86921400-86923000	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr4:86921600-86923000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr4:86921600-86923200	Strong transcription	Primary B cells from cord blood	blood

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