Variant report

Variant	rs60810860
Chromosome Location	chr2:86724908-86724909
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	chr2:86720517..86722121-chr2:86723212..86725706,2	K562	blood:
2	chr2:86720341..86722407-chr2:86724543..86726613,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1030886	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1030887	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11127043	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11548929	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11891659	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11899532	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1437614	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1518808	0.93[EUR][1000 genomes]
rs1518810	0.91[EUR][1000 genomes]
rs1518812	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17027265	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17027270	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17027280	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17027296	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34605051	0.96[EUR][1000 genomes]
rs34633268	0.91[EUR][1000 genomes]
rs55688177	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs55708352	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55828608	0.93[EUR][1000 genomes]
rs56055358	0.96[EUR][1000 genomes]
rs56085540	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56169889	0.93[EUR][1000 genomes]
rs56211578	0.83[EUR][1000 genomes]
rs56227180	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56242451	0.91[EUR][1000 genomes]
rs56347930	0.93[EUR][1000 genomes]
rs57291816	0.93[EUR][1000 genomes]
rs57836876	0.96[EUR][1000 genomes]
rs58091125	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs58361202	0.93[EUR][1000 genomes]
rs58829418	0.96[EUR][1000 genomes]
rs59026369	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs59183618	0.93[EUR][1000 genomes]
rs59255035	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59336972	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59521243	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs59613942	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs59859947	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs59895355	0.85[EUR][1000 genomes]
rs60073472	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs60244636	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs60304516	0.93[EUR][1000 genomes]
rs60717666	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60796561	0.85[EUR][1000 genomes]
rs61028062	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61465748	0.85[EUR][1000 genomes]
rs61547860	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6710780	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6720414	0.85[EUR][1000 genomes]
rs6740863	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6745875	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72930315	0.93[EUR][1000 genomes]
rs72930323	0.93[EUR][1000 genomes]
rs72930336	0.93[EUR][1000 genomes]
rs72930340	0.93[EUR][1000 genomes]
rs72930349	0.93[EUR][1000 genomes]
rs72930361	0.93[EUR][1000 genomes]
rs72930362	0.93[EUR][1000 genomes]
rs72930364	0.93[EUR][1000 genomes]
rs72930369	0.93[EUR][1000 genomes]
rs72930387	0.96[EUR][1000 genomes]
rs72930396	0.94[EUR][1000 genomes]
rs72930400	0.93[EUR][1000 genomes]
rs72932307	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72932310	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72932311	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72932316	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72932319	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72932336	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72932350	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72932358	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72932364	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72932369	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs72932380	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7562493	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7585722	0.85[EUR][1000 genomes]
rs7586028	0.85[EUR][1000 genomes]
rs7604179	0.89[EUR][1000 genomes]
rs7608800	0.90[AFR][1000 genomes];0.89[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60810860	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86671000-86725600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:86671400-86725600	Strong transcription	A549	lung
3	chr2:86671600-86726000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:86671800-86726600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:86674200-86726800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:86676600-86727200	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:86681600-86727000	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr2:86682000-86726600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:86682200-86726200	Strong transcription	Fetal Lung	lung
11	chr2:86684000-86726000	Strong transcription	Duodenum Mucosa	Duodenum
12	chr2:86696000-86727000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr2:86697600-86727200	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr2:86697800-86728800	Strong transcription	Primary T cells from cord blood	blood
15	chr2:86699400-86727000	Strong transcription	Placenta	Placenta
16	chr2:86701000-86725600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:86704800-86726400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:86704800-86726600	Strong transcription	NHDF-Ad	bronchial
19	chr2:86708800-86726600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:86709200-86726600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:86709200-86737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:86709800-86725600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:86712800-86726600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:86713400-86727400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:86716600-86725200	Weak transcription	Aorta	Aorta
26	chr2:86717200-86726600	Weak transcription	Pancreas	Pancrea
27	chr2:86717400-86726600	Weak transcription	Stomach Mucosa	stomach
28	chr2:86718600-86725200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:86718800-86726600	Weak transcription	Gastric	stomach
30	chr2:86718800-86726600	Weak transcription	Right Ventricle	heart
31	chr2:86719400-86725200	Weak transcription	NHEK	skin
32	chr2:86719400-86726000	Strong transcription	HSMM	muscle
33	chr2:86719400-86726600	Weak transcription	Spleen	Spleen
34	chr2:86719800-86725200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:86719800-86725400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr2:86719800-86725400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:86719800-86725400	Weak transcription	K562	blood
38	chr2:86719800-86726600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr2:86719800-86726800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:86719800-86726800	Strong transcription	Liver	Liver
41	chr2:86719800-86726800	Weak transcription	Esophagus	oesophagus
42	chr2:86719800-86734600	Weak transcription	Psoas Muscle	Psoas
43	chr2:86720000-86725400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:86720000-86725400	Weak transcription	HSMMtube	muscle
45	chr2:86720200-86725200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:86720200-86725600	Weak transcription	Fetal Heart	heart
47	chr2:86720400-86726600	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr2:86720400-86727000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:86720600-86725800	Weak transcription	Hela-S3	cervix
50	chr2:86720600-86726000	Weak transcription	Brain Anterior Caudate	brain

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