Variant report

Variant	rs60073472
Chromosome Location	chr2:86780540-86780541
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86777618..86781081-chr2:86786996..86791051,3	K562	blood:
2	chr2:86666646..86669361-chr2:86779327..86781244,2	K562	blood:

Variant related genes	Relation type
ENSG00000115548	Chromatin interaction
ENSG00000228363	Chromatin interaction
ENSG00000115561	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1030886	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1030887	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11127043	0.95[EUR][1000 genomes]
rs11548929	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11890032	0.85[EUR][1000 genomes]
rs11891659	0.96[EUR][1000 genomes]
rs11899532	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1437614	0.89[EUR][1000 genomes]
rs1518808	0.87[EUR][1000 genomes]
rs1518810	0.85[EUR][1000 genomes]
rs1518812	0.87[EUR][1000 genomes]
rs17027265	0.87[EUR][1000 genomes]
rs17027270	0.87[EUR][1000 genomes]
rs17027280	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs17027296	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34605051	0.85[EUR][1000 genomes]
rs34633268	0.87[EUR][1000 genomes]
rs55688177	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55708352	0.96[EUR][1000 genomes]
rs55828608	0.87[EUR][1000 genomes]
rs56055358	0.85[EUR][1000 genomes]
rs56085540	0.87[EUR][1000 genomes]
rs56169889	0.87[EUR][1000 genomes]
rs56211578	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56227180	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56242451	0.85[EUR][1000 genomes]
rs56347930	0.87[EUR][1000 genomes]
rs56378606	0.94[EUR][1000 genomes]
rs57291816	0.87[EUR][1000 genomes]
rs57836876	0.85[EUR][1000 genomes]
rs58091125	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58361202	0.87[EUR][1000 genomes]
rs58829418	0.85[EUR][1000 genomes]
rs59026369	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59183618	0.83[EUR][1000 genomes]
rs59255035	0.85[EUR][1000 genomes]
rs59336972	0.87[EUR][1000 genomes]
rs59521243	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59613942	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59859947	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59895355	1.00[EUR][1000 genomes]
rs60244636	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60304516	0.87[EUR][1000 genomes]
rs60717666	0.85[EUR][1000 genomes]
rs60796561	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60810860	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61028062	0.87[EUR][1000 genomes]
rs61465748	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61547860	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6710780	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6720414	1.00[EUR][1000 genomes]
rs6740863	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6745875	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs72930315	0.87[EUR][1000 genomes]
rs72930323	0.87[EUR][1000 genomes]
rs72930336	0.87[EUR][1000 genomes]
rs72930340	0.87[EUR][1000 genomes]
rs72930349	0.87[EUR][1000 genomes]
rs72930361	0.87[EUR][1000 genomes]
rs72930362	0.87[EUR][1000 genomes]
rs72930364	0.87[EUR][1000 genomes]
rs72930369	0.87[EUR][1000 genomes]
rs72930387	0.85[EUR][1000 genomes]
rs72930396	0.83[EUR][1000 genomes]
rs72930400	0.83[EUR][1000 genomes]
rs72932307	0.85[EUR][1000 genomes]
rs72932310	0.87[EUR][1000 genomes]
rs72932311	0.87[EUR][1000 genomes]
rs72932316	0.87[EUR][1000 genomes]
rs72932319	0.87[EUR][1000 genomes]
rs72932336	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs72932350	0.96[EUR][1000 genomes]
rs72932358	0.96[EUR][1000 genomes]
rs72932364	0.96[EUR][1000 genomes]
rs72932369	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72932380	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73949838	0.94[EUR][1000 genomes]
rs73949839	0.94[EUR][1000 genomes]
rs7562493	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7585722	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7586028	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7604179	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7608800	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv829488	chr2:86769108-86780946	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60073472	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86734000-86784800	Weak transcription	Osteobl	bone
2	chr2:86737400-86788400	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:86753800-86788400	Weak transcription	HSMM	muscle
4	chr2:86756000-86788400	Weak transcription	Brain Anterior Caudate	brain
5	chr2:86756600-86784800	Weak transcription	Left Ventricle	heart
6	chr2:86756600-86789200	Weak transcription	Aorta	Aorta
7	chr2:86761200-86788600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:86761200-86788800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:86768200-86785000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:86768800-86784200	Weak transcription	Psoas Muscle	Psoas
11	chr2:86768800-86785200	Weak transcription	Stomach Mucosa	stomach
12	chr2:86769400-86785600	Weak transcription	Fetal Heart	heart
13	chr2:86771200-86788400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:86771400-86786200	Weak transcription	HSMMtube	muscle
15	chr2:86773200-86781400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:86773400-86784200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:86774200-86788200	Weak transcription	Adipose Nuclei	Adipose
18	chr2:86774400-86788800	Weak transcription	Fetal Lung	lung
19	chr2:86774600-86788200	Weak transcription	Hela-S3	cervix
20	chr2:86774800-86785200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:86775200-86782600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:86775200-86784200	Weak transcription	A549	lung
23	chr2:86775200-86784800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:86775200-86785200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:86775200-86788200	Weak transcription	K562	blood
26	chr2:86775200-86788800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr2:86775400-86782800	Weak transcription	HepG2	liver
28	chr2:86776000-86780600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
29	chr2:86776800-86788800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:86777000-86784600	Weak transcription	Right Ventricle	heart
31	chr2:86777000-86787800	Weak transcription	Ovary	ovary
32	chr2:86777000-86788000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:86777200-86783800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr2:86777400-86789200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:86777400-86789600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:86777600-86783400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:86777600-86783600	Weak transcription	Thymus	Thymus
38	chr2:86777600-86784800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:86777600-86784800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:86777600-86785400	Weak transcription	Spleen	Spleen
41	chr2:86777600-86785600	Weak transcription	Gastric	stomach
42	chr2:86777600-86785800	Weak transcription	Pancreas	Pancrea
43	chr2:86777600-86786400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:86777600-86788000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:86777600-86788200	Weak transcription	Liver	Liver
46	chr2:86777600-86789200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:86777600-86789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:86777600-86789400	Weak transcription	Lung	lung
49	chr2:86777800-86787800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:86777800-86788400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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