Variant report

Variant	rs55708352
Chromosome Location	chr2:86741441-86741442
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	chr2:86665985..86667815-chr2:86739595..86741738,2	K562	blood:
2	chr2:86735334..86737957-chr2:86740188..86742060,2	K562	blood:

Variant related genes	Relation type
ENSG00000115548	Chromatin interaction

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

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

rs_ID	r²[population]
rs1030886	1.00[EUR][1000 genomes]
rs1030887	1.00[EUR][1000 genomes]
rs11127043	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11548929	1.00[EUR][1000 genomes]
rs11890032	0.89[EUR][1000 genomes]
rs11891659	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11899532	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1437614	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1518808	0.91[EUR][1000 genomes]
rs1518810	0.89[EUR][1000 genomes]
rs1518812	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027265	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027270	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027280	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027296	0.96[EUR][1000 genomes]
rs34605051	0.89[EUR][1000 genomes]
rs34633268	0.91[EUR][1000 genomes]
rs55688177	1.00[EUR][1000 genomes]
rs55828608	0.91[EUR][1000 genomes]
rs56055358	0.89[EUR][1000 genomes]
rs56085540	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56169889	0.91[EUR][1000 genomes]
rs56211578	0.93[EUR][1000 genomes]
rs56227180	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	0.96[EUR][1000 genomes]
rs58361202	0.91[EUR][1000 genomes]
rs58829418	0.89[EUR][1000 genomes]
rs59026369	0.96[EUR][1000 genomes]
rs59183618	0.87[EUR][1000 genomes]
rs59255035	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59336972	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59521243	0.96[EUR][1000 genomes]
rs59613942	0.96[EUR][1000 genomes]
rs59859947	0.96[EUR][1000 genomes]
rs59895355	0.96[EUR][1000 genomes]
rs60073472	0.96[EUR][1000 genomes]
rs60244636	0.96[EUR][1000 genomes]
rs60304516	0.91[EUR][1000 genomes]
rs60717666	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60796561	0.96[EUR][1000 genomes]
rs60810860	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61028062	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61465748	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61547860	1.00[EUR][1000 genomes]
rs6710780	1.00[EUR][1000 genomes]
rs6720414	0.96[EUR][1000 genomes]
rs6740863	1.00[EUR][1000 genomes]
rs6745875	0.97[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	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72932310	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932311	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932316	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932319	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932336	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932350	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932358	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932364	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932369	1.00[EUR][1000 genomes]
rs72932380	0.96[EUR][1000 genomes]
rs73949838	0.90[EUR][1000 genomes]
rs73949839	0.90[EUR][1000 genomes]
rs7562493	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7585722	0.96[EUR][1000 genomes]
rs7586028	0.96[EUR][1000 genomes]
rs7604179	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7608800	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
rs55708352	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:86726400-86741800	Weak transcription	NH-A	brain
3	chr2:86726400-86753000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:86726600-86748600	Weak transcription	Hela-S3	cervix
5	chr2:86728200-86755800	Weak transcription	Fetal Brain Male	brain
6	chr2:86728400-86747200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:86729000-86747000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:86732400-86745000	Weak transcription	Fetal Kidney	kidney
9	chr2:86733000-86759400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:86733400-86758600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:86734000-86784800	Weak transcription	Osteobl	bone
12	chr2:86736400-86770600	Weak transcription	Brain Angular Gyrus	brain
13	chr2:86736800-86754400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:86737000-86743600	Weak transcription	Fetal Brain Female	brain
15	chr2:86737000-86747200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:86737000-86752600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr2:86737000-86753000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:86737000-86754400	Weak transcription	NHDF-Ad	bronchial
19	chr2:86737000-86761200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:86737000-86772800	Weak transcription	Pancreas	Pancrea
21	chr2:86737200-86745400	Weak transcription	Brain Anterior Caudate	brain
22	chr2:86737200-86746200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:86737200-86746600	Weak transcription	GM12878-XiMat	blood
24	chr2:86737200-86746800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:86737200-86747000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:86737200-86747400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr2:86737200-86747600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:86737200-86751600	Weak transcription	HSMM	muscle
29	chr2:86737400-86747400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:86737400-86747400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:86737400-86747400	Weak transcription	Esophagus	oesophagus
32	chr2:86737400-86749000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:86737400-86753000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:86737400-86755400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:86737400-86756800	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:86737400-86757400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr2:86737400-86788400	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:86737600-86742200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr2:86737600-86745600	Weak transcription	Fetal Stomach	stomach
40	chr2:86737600-86746200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:86737600-86746600	Weak transcription	NHLF	lung
42	chr2:86737600-86747000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:86737600-86747200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:86737600-86747400	Weak transcription	Adipose Nuclei	Adipose
45	chr2:86737600-86747800	Weak transcription	Gastric	stomach
46	chr2:86737600-86748800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:86737600-86768400	Weak transcription	Ovary	ovary
48	chr2:86737800-86747200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:86737800-86747200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:86737800-86747400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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