Variant report

Variant	rs55688177
Chromosome Location	chr2:86757210-86757211
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	chr2:86755933..86757641-chr2:86759393..86762137,2	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]
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]
rs61547860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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
rs55688177	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86733000-86759400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:86733400-86758600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:86734000-86784800	Weak transcription	Osteobl	bone
4	chr2:86736400-86770600	Weak transcription	Brain Angular Gyrus	brain
5	chr2:86737000-86761200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:86737000-86772800	Weak transcription	Pancreas	Pancrea
7	chr2:86737400-86757400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:86737400-86788400	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:86737600-86768400	Weak transcription	Ovary	ovary
10	chr2:86737800-86779600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:86738200-86772400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:86738200-86772600	Weak transcription	Right Ventricle	heart
13	chr2:86738400-86759000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr2:86741400-86768400	Weak transcription	Psoas Muscle	Psoas
15	chr2:86746000-86768000	Weak transcription	Fetal Heart	heart
16	chr2:86748000-86758000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:86748000-86758000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:86748000-86758600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:86748000-86760600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:86748000-86770600	Weak transcription	Gastric	stomach
21	chr2:86748200-86759000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr2:86749400-86772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:86749400-86775000	Weak transcription	NH-A	brain
24	chr2:86749600-86757800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:86750000-86772400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:86750400-86773600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:86753400-86758600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr2:86753600-86761600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr2:86753800-86759200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr2:86753800-86788400	Weak transcription	HSMM	muscle
31	chr2:86754000-86774000	Weak transcription	Hela-S3	cervix
32	chr2:86754400-86758200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:86754600-86758600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr2:86755200-86759200	Weak transcription	Fetal Thymus	thymus
35	chr2:86755600-86760600	Weak transcription	Fetal Intestine Small	intestine
36	chr2:86755600-86761600	Weak transcription	HUVEC	blood vessel
37	chr2:86755800-86759600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:86756000-86758600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:86756000-86758800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:86756000-86758800	Weak transcription	A549	lung
41	chr2:86756000-86788400	Weak transcription	Brain Anterior Caudate	brain
42	chr2:86756200-86758800	Weak transcription	Small Intestine	intestine
43	chr2:86756200-86759000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr2:86756200-86759000	Weak transcription	Brain Germinal Matrix	brain
45	chr2:86756200-86759800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:86756400-86758800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr2:86756400-86759000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:86756400-86759000	Weak transcription	Dnd41	blood
49	chr2:86756400-86759200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:86756400-86759400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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