Variant report

Variant	rs11899532
Chromosome Location	chr2:86723016-86723017
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86700841..86702397-chr2:86722250..86724603,2	MCF-7	breast:
2	chr2:86708605..86710525-chr2:86722087..86724639,2	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1030886	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1030887	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11127043	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11548929	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11890032	0.81[EUR][1000 genomes]
rs11891659	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1437614	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1518808	0.96[EUR][1000 genomes]
rs1518810	0.93[EUR][1000 genomes]
rs1518812	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027265	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027270	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027280	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027296	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34605051	0.98[EUR][1000 genomes]
rs34633268	0.93[EUR][1000 genomes]
rs55688177	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55708352	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55828608	0.96[EUR][1000 genomes]
rs56055358	0.98[EUR][1000 genomes]
rs56085540	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56169889	0.96[EUR][1000 genomes]
rs56211578	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56227180	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56242451	0.93[EUR][1000 genomes]
rs56347930	0.96[EUR][1000 genomes]
rs56378606	0.82[EUR][1000 genomes]
rs57291816	0.96[EUR][1000 genomes]
rs57836876	0.98[EUR][1000 genomes]
rs58091125	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58361202	0.96[EUR][1000 genomes]
rs58829418	0.98[EUR][1000 genomes]
rs59026369	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59183618	0.96[EUR][1000 genomes]
rs59255035	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59336972	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59521243	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs59613942	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59859947	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs59895355	0.87[EUR][1000 genomes]
rs60073472	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs60244636	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60304516	0.96[EUR][1000 genomes]
rs60717666	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60796561	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60810860	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61028062	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61465748	0.87[EUR][1000 genomes]
rs61547860	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6710780	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6720414	0.87[EUR][1000 genomes]
rs6740863	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6745875	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72930315	0.96[EUR][1000 genomes]
rs72930323	0.96[EUR][1000 genomes]
rs72930336	0.96[EUR][1000 genomes]
rs72930340	0.96[EUR][1000 genomes]
rs72930349	0.96[EUR][1000 genomes]
rs72930361	0.96[EUR][1000 genomes]
rs72930362	0.96[EUR][1000 genomes]
rs72930364	0.96[EUR][1000 genomes]
rs72930369	0.96[EUR][1000 genomes]
rs72930387	0.98[EUR][1000 genomes]
rs72930396	0.96[EUR][1000 genomes]
rs72930400	0.96[EUR][1000 genomes]
rs72932307	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72932310	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932311	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932316	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932319	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932336	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932350	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932358	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932364	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932369	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932380	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73949838	0.82[EUR][1000 genomes]
rs73949839	0.82[EUR][1000 genomes]
rs7562493	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7585722	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7586028	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7604179	0.91[EUR][1000 genomes]
rs7608800	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[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
rs11899532	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 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	chr2:86671600-86723600	Strong transcription	Fetal Thymus	thymus
4	chr2:86671600-86726000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:86671800-86726600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:86672600-86724200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:86674200-86726800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:86676600-86727200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:86681600-86727000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr2:86682000-86726600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:86682200-86726200	Strong transcription	Fetal Lung	lung
13	chr2:86684000-86726000	Strong transcription	Duodenum Mucosa	Duodenum
14	chr2:86690200-86723200	Strong transcription	Primary B cells from cord blood	blood
15	chr2:86696000-86727000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr2:86697200-86724600	Strong transcription	Dnd41	blood
17	chr2:86697600-86727200	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:86697800-86728800	Strong transcription	Primary T cells from cord blood	blood
19	chr2:86699400-86727000	Strong transcription	Placenta	Placenta
20	chr2:86701000-86725600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:86704800-86726400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:86704800-86726600	Strong transcription	NHDF-Ad	bronchial
23	chr2:86706000-86724400	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:86708800-86726600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:86709200-86726600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:86709200-86737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:86709800-86725600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:86712800-86726600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:86713400-86727400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:86716200-86724600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:86716600-86725200	Weak transcription	Aorta	Aorta
32	chr2:86717000-86724400	Weak transcription	Fetal Brain Male	brain
33	chr2:86717200-86726600	Weak transcription	Pancreas	Pancrea
34	chr2:86717400-86726600	Weak transcription	Stomach Mucosa	stomach
35	chr2:86718000-86723800	Weak transcription	Brain Germinal Matrix	brain
36	chr2:86718400-86724200	Weak transcription	Colonic Mucosa	Colon
37	chr2:86718600-86725200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:86718800-86724400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:86718800-86724400	Weak transcription	Brain Angular Gyrus	brain
40	chr2:86718800-86726600	Weak transcription	Gastric	stomach
41	chr2:86718800-86726600	Weak transcription	Right Ventricle	heart
42	chr2:86719200-86724200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr2:86719200-86724400	Weak transcription	Lung	lung
44	chr2:86719400-86725200	Weak transcription	NHEK	skin
45	chr2:86719400-86726000	Strong transcription	HSMM	muscle
46	chr2:86719400-86726600	Weak transcription	Spleen	Spleen
47	chr2:86719800-86723600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr2:86719800-86723600	Weak transcription	Fetal Intestine Small	intestine
49	chr2:86719800-86723600	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:86719800-86724400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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