Variant report

Variant	rs12650390
Chromosome Location	chr4:86863032-86863033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:86858002..86860369-chr4:86861620..86863403,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10003909	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10305	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1075824	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097083	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097084	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097086	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11097088	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097089	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11547776	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11724577	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12500273	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12503695	0.87[EUR][1000 genomes]
rs12504340	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12505097	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12507178	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12510562	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12510563	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13102197	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13104099	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13110329	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13116843	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13118404	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13121803	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13127513	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13130578	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13137855	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13138054	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13141273	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13142650	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13144829	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13149026	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13149606	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13149705	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1436528	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17011215	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2118042	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2118043	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2164534	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2904086	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35817700	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35832919	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35922412	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3943729	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3943730	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4693133	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4693134	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4693752	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531887	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531888	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66778815	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6813736	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6815772	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6821120	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6825252	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6825488	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6838333	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6848107	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7442034	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7679822	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7686475	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7688039	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs934648	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9685083	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs996804	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9996062	0.91[EUR][1000 genomes];0.95[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	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	nsv879519	chr4:86786204-86871282	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12650390	RP11-778J15.1	cis	Artery Tibial	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86851200-86863200	Weak transcription	Psoas Muscle	Psoas
2	chr4:86851400-86865800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr4:86851400-86874600	Weak transcription	HSMMtube	muscle
4	chr4:86851600-86870000	Weak transcription	HSMM	muscle
5	chr4:86851600-86874800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:86853800-86864400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:86854000-86867400	Weak transcription	Fetal Lung	lung
8	chr4:86854000-86874200	Weak transcription	Fetal Stomach	stomach
9	chr4:86854000-86893000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr4:86854200-86863200	Weak transcription	Pancreas	Pancrea
11	chr4:86854200-86880200	Weak transcription	Gastric	stomach
12	chr4:86854200-86893000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr4:86854200-86915800	Weak transcription	Left Ventricle	heart
14	chr4:86854800-86863200	Weak transcription	Fetal Muscle Leg	muscle
15	chr4:86856000-86863200	Weak transcription	Right Atrium	heart
16	chr4:86858400-86863600	Enhancers	Fetal Kidney	kidney
17	chr4:86858800-86876600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:86859600-86874200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:86860200-86867400	Weak transcription	Primary B cells from cord blood	blood
20	chr4:86860400-86863200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:86860400-86867600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:86860400-86874800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:86861200-86865800	Weak transcription	Osteobl	bone
24	chr4:86861200-86873400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:86861600-86863200	Weak transcription	Ovary	ovary
26	chr4:86861600-86864400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr4:86861800-86864800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:86861800-86870000	Weak transcription	NHLF	lung
29	chr4:86861800-86873400	Weak transcription	NHDF-Ad	bronchial
30	chr4:86862200-86870800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:86862400-86877200	Weak transcription	Liver	Liver
32	chr4:86862600-86864600	Enhancers	Dnd41	blood
33	chr4:86863000-86863600	Strong transcription	HUVEC	blood vessel
34	chr4:86863000-86863800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:86863000-86864000	Enhancers	Primary neutrophils fromperipheralblood	blood

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