Variant report

Variant	rs11547776
Chromosome Location	chr4:86915923-86915924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10003909	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10305	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1075824	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097083	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11097084	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11097086	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097088	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097089	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11724577	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500273	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12503695	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12504340	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12505097	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12507178	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12510562	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12510563	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12650390	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13102197	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13104099	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13110329	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13116843	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13118404	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13121803	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13127513	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13130578	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13137855	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13138054	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13141273	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13142650	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13144829	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13149026	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13149606	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13149705	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1436528	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17011215	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2118042	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2118043	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2164534	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2904086	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35817700	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35832919	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35922412	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3943729	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3943730	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4693133	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4693134	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4693752	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531887	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6531888	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66778815	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813736	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6815772	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821120	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6825252	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6825488	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6838333	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6848107	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72660176	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7442034	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7679822	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686475	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688039	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs934648	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9685083	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs996804	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9996062	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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
2	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
3	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
rs11547776	RP11-778J15.1	cis	Artery Tibial	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86888800-86919200	Weak transcription	Colon Smooth Muscle	Colon
2	chr4:86889400-86935000	Weak transcription	Psoas Muscle	Psoas
3	chr4:86890400-86916000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:86892000-86916000	Weak transcription	Spleen	Spleen
5	chr4:86897600-86916000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr4:86897600-86916400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr4:86899200-86927000	Weak transcription	Lung	lung
8	chr4:86899800-86917800	Weak transcription	Small Intestine	intestine
9	chr4:86906400-86916000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:86907800-86916000	Weak transcription	Osteobl	bone
11	chr4:86911000-86919400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:86911800-86916000	Weak transcription	NHLF	lung
13	chr4:86913000-86918200	Strong transcription	Primary B cells from peripheral blood	blood
14	chr4:86913200-86919000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr4:86913800-86916000	Weak transcription	HSMM	muscle
16	chr4:86914000-86916200	Weak transcription	Brain Hippocampus Middle	brain
17	chr4:86914200-86924000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:86914400-86916000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:86914400-86917800	Strong transcription	Fetal Muscle Leg	muscle
20	chr4:86914600-86917800	Strong transcription	NHDF-Ad	bronchial
21	chr4:86914800-86917600	Weak transcription	Stomach Mucosa	stomach
22	chr4:86914800-86918400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr4:86914800-86923200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr4:86915200-86918000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:86915200-86918200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:86915600-86916200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:86915600-86916800	Genic enhancers	HUVEC	blood vessel
28	chr4:86915600-86917000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:86915600-86917000	Strong transcription	Fetal Lung	lung
30	chr4:86915600-86917000	Strong transcription	Placenta	Placenta
31	chr4:86915600-86917200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:86915600-86917400	Strong transcription	Stomach Smooth Muscle	stomach
33	chr4:86915600-86917800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr4:86915600-86918200	Strong transcription	Primary B cells from cord blood	blood
35	chr4:86915800-86916000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:86915800-86916000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr4:86915800-86916000	Genic enhancers	Gastric	stomach
38	chr4:86915800-86916600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:86915800-86916600	Strong transcription	Fetal Intestine Small	intestine
40	chr4:86915800-86916800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:86915800-86916800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr4:86915800-86916800	Strong transcription	Ovary	ovary
43	chr4:86915800-86917000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:86915800-86917000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:86915800-86917000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr4:86915800-86917000	Strong transcription	Aorta	Aorta
47	chr4:86915800-86917000	Strong transcription	Left Ventricle	heart
48	chr4:86915800-86917000	Strong transcription	Pancreas	Pancrea
49	chr4:86915800-86917000	Strong transcription	Right Ventricle	heart
50	chr4:86915800-86917000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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