Variant report

Variant	rs61547860
Chromosome Location	chr2:86768170-86768171
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86760228..86762671-chr2:86766601..86768466,2	MCF-7	breast:
2	chr2:86745280..86747969-chr2:86766935..86768538,2	MCF-7	breast:
3	chr2:86759845..86761592-chr2:86766001..86768236,2	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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1030887	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11127043	0.99[EUR][1000 genomes]
rs11548929	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11890032	0.89[EUR][1000 genomes]
rs11891659	1.00[EUR][1000 genomes]
rs11899532	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1437614	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1518808	0.91[EUR][1000 genomes]
rs1518810	0.89[EUR][1000 genomes]
rs1518812	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027265	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027270	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027280	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027296	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34605051	0.89[EUR][1000 genomes]
rs34633268	0.91[EUR][1000 genomes]
rs55688177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55708352	1.00[EUR][1000 genomes]
rs55828608	0.91[EUR][1000 genomes]
rs56055358	0.89[EUR][1000 genomes]
rs56085540	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56169889	0.91[EUR][1000 genomes]
rs56211578	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56227180	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56242451	0.89[EUR][1000 genomes]
rs56347930	0.91[EUR][1000 genomes]
rs56378606	0.90[EUR][1000 genomes]
rs57291816	0.91[EUR][1000 genomes]
rs57836876	0.89[EUR][1000 genomes]
rs58091125	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58361202	0.91[EUR][1000 genomes]
rs58829418	0.89[EUR][1000 genomes]
rs59026369	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59183618	0.87[EUR][1000 genomes]
rs59255035	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59336972	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59521243	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59613942	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59859947	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59895355	0.96[EUR][1000 genomes]
rs60073472	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60244636	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60304516	0.91[EUR][1000 genomes]
rs60717666	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60796561	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60810860	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs61028062	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61465748	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6710780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6720414	0.96[EUR][1000 genomes]
rs6740863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6745875	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930315	0.91[EUR][1000 genomes]
rs72930323	0.91[EUR][1000 genomes]
rs72930336	0.91[EUR][1000 genomes]
rs72930340	0.91[EUR][1000 genomes]
rs72930349	0.91[EUR][1000 genomes]
rs72930361	0.91[EUR][1000 genomes]
rs72930362	0.91[EUR][1000 genomes]
rs72930364	0.91[EUR][1000 genomes]
rs72930369	0.91[EUR][1000 genomes]
rs72930387	0.89[EUR][1000 genomes]
rs72930396	0.87[EUR][1000 genomes]
rs72930400	0.87[EUR][1000 genomes]
rs72932307	0.89[EUR][1000 genomes]
rs72932310	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932311	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932316	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932319	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932336	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932350	1.00[EUR][1000 genomes]
rs72932358	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932364	1.00[EUR][1000 genomes]
rs72932369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932380	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73949838	0.90[EUR][1000 genomes]
rs73949839	0.90[EUR][1000 genomes]
rs7562493	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7585722	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7586028	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7604179	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7608800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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
rs61547860	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86734000-86784800	Weak transcription	Osteobl	bone
2	chr2:86736400-86770600	Weak transcription	Brain Angular Gyrus	brain
3	chr2:86737000-86772800	Weak transcription	Pancreas	Pancrea
4	chr2:86737400-86788400	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:86737600-86768400	Weak transcription	Ovary	ovary
6	chr2:86737800-86779600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:86738200-86772400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:86738200-86772600	Weak transcription	Right Ventricle	heart
9	chr2:86741400-86768400	Weak transcription	Psoas Muscle	Psoas
10	chr2:86748000-86770600	Weak transcription	Gastric	stomach
11	chr2:86749400-86772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:86749400-86775000	Weak transcription	NH-A	brain
13	chr2:86750000-86772400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:86750400-86773600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:86753800-86788400	Weak transcription	HSMM	muscle
16	chr2:86754000-86774000	Weak transcription	Hela-S3	cervix
17	chr2:86756000-86788400	Weak transcription	Brain Anterior Caudate	brain
18	chr2:86756400-86772600	Weak transcription	Lung	lung
19	chr2:86756400-86773800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr2:86756600-86770400	Weak transcription	Liver	Liver
21	chr2:86756600-86770400	Weak transcription	HepG2	liver
22	chr2:86756600-86771800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:86756600-86772400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:86756600-86772400	Weak transcription	Thymus	Thymus
25	chr2:86756600-86772600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:86756600-86773200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:86756600-86773600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:86756600-86776200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:86756600-86779000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr2:86756600-86779000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr2:86756600-86784800	Weak transcription	Left Ventricle	heart
32	chr2:86756600-86789200	Weak transcription	Aorta	Aorta
33	chr2:86756800-86772600	Weak transcription	Placenta	Placenta
34	chr2:86756800-86779400	Weak transcription	NHDF-Ad	bronchial
35	chr2:86757000-86773000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:86761200-86788600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:86761200-86788800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:86761400-86768200	Weak transcription	Adipose Nuclei	Adipose
39	chr2:86761400-86769000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:86761400-86779400	Weak transcription	NHEK	skin
41	chr2:86761600-86772600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:86761800-86772800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr2:86761800-86773800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:86762800-86771800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:86763200-86771000	Weak transcription	A549	lung
46	chr2:86764200-86770000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:86764400-86768400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:86764600-86768400	Weak transcription	Esophagus	oesophagus
49	chr2:86764600-86779600	Weak transcription	HMEC	breast
50	chr2:86764800-86771400	Enhancers	Primary neutrophils fromperipheralblood	blood

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