Variant report

Variant	rs57836876
Chromosome Location	chr2:86693217-86693218
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86668149..86671762-chr2:86690412..86696565,6	K562	blood:
2	chr2:86683189..86686593-chr2:86691402..86694661,3	K562	blood:

Variant related genes	Relation type
ENSG00000115548	Chromatin interaction

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

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

rs_ID	r²[population]
rs1030886	0.89[EUR][1000 genomes]
rs1030887	0.89[EUR][1000 genomes]
rs11127043	0.88[EUR][1000 genomes]
rs11548929	0.89[EUR][1000 genomes]
rs11891659	0.89[EUR][1000 genomes]
rs11899532	0.98[EUR][1000 genomes]
rs1437614	0.96[EUR][1000 genomes]
rs1518808	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1518810	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1518812	0.98[EUR][1000 genomes]
rs17027265	0.98[EUR][1000 genomes]
rs17027270	0.98[EUR][1000 genomes]
rs17027280	0.89[EUR][1000 genomes]
rs17027296	0.85[EUR][1000 genomes]
rs34605051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34633268	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55688177	0.89[EUR][1000 genomes]
rs55708352	0.89[EUR][1000 genomes]
rs55828608	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56055358	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56085540	0.98[EUR][1000 genomes]
rs56169889	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56211578	0.83[EUR][1000 genomes]
rs56227180	0.85[EUR][1000 genomes]
rs56242451	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56347930	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57291816	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58091125	0.85[EUR][1000 genomes]
rs58361202	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58829418	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59026369	0.85[EUR][1000 genomes]
rs59183618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59255035	1.00[EUR][1000 genomes]
rs59336972	0.98[EUR][1000 genomes]
rs59521243	0.85[EUR][1000 genomes]
rs59613942	0.85[EUR][1000 genomes]
rs59859947	0.85[EUR][1000 genomes]
rs59895355	0.85[EUR][1000 genomes]
rs60073472	0.85[EUR][1000 genomes]
rs60244636	0.85[EUR][1000 genomes]
rs60304516	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60717666	1.00[EUR][1000 genomes]
rs60796561	0.85[EUR][1000 genomes]
rs60810860	0.96[EUR][1000 genomes]
rs61028062	0.98[EUR][1000 genomes]
rs61465748	0.85[EUR][1000 genomes]
rs61547860	0.89[EUR][1000 genomes]
rs6710780	0.89[EUR][1000 genomes]
rs6720414	0.85[EUR][1000 genomes]
rs6740863	0.89[EUR][1000 genomes]
rs6745875	0.89[EUR][1000 genomes]
rs72930315	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930323	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930336	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930340	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930349	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930361	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930362	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930369	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930387	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930396	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72930400	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72932307	1.00[EUR][1000 genomes]
rs72932310	0.98[EUR][1000 genomes]
rs72932311	0.98[EUR][1000 genomes]
rs72932316	0.98[EUR][1000 genomes]
rs72932319	0.98[EUR][1000 genomes]
rs72932336	0.89[EUR][1000 genomes]
rs72932350	0.89[EUR][1000 genomes]
rs72932358	0.89[EUR][1000 genomes]
rs72932364	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72932369	0.89[EUR][1000 genomes]
rs72932380	0.85[EUR][1000 genomes]
rs7562493	0.89[EUR][1000 genomes]
rs7585722	0.85[EUR][1000 genomes]
rs7586028	0.85[EUR][1000 genomes]
rs7604179	0.89[EUR][1000 genomes]
rs7608800	0.89[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
rs57836876	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86670400-86693400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:86671000-86725600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:86671400-86722600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:86671400-86725600	Strong transcription	A549	lung
5	chr2:86671600-86695400	Strong transcription	HSMM	muscle
6	chr2:86671600-86719800	Strong transcription	Primary B cells from peripheral blood	blood
7	chr2:86671600-86723600	Strong transcription	Fetal Thymus	thymus
8	chr2:86671600-86726000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:86671800-86726600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr2:86672600-86721200	Strong transcription	Fetal Intestine Large	intestine
11	chr2:86672600-86724200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:86674200-86726800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:86674600-86721400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr2:86674800-86695000	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr2:86675400-86694600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:86676400-86693600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:86676400-86722600	Strong transcription	GM12878-XiMat	blood
18	chr2:86676600-86695600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:86676600-86721600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:86676600-86727200	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:86676800-86698200	Strong transcription	Placenta	Placenta
22	chr2:86676800-86701000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:86676800-86703800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:86677000-86705200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:86677200-86708200	Strong transcription	HepG2	liver
26	chr2:86677200-86709200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr2:86679400-86708000	Strong transcription	Primary hematopoietic stem cells	blood
28	chr2:86679600-86721400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:86679600-86721800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr2:86680200-86722200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:86681000-86720800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr2:86681600-86699600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:86681600-86722600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:86681600-86727000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr2:86681800-86699000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:86681800-86702600	Strong transcription	NHDF-Ad	bronchial
38	chr2:86681800-86703600	Strong transcription	Liver	Liver
39	chr2:86682000-86702400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:86682000-86707000	Strong transcription	Adipose Nuclei	Adipose
41	chr2:86682000-86718600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr2:86682000-86726600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:86682200-86726200	Strong transcription	Fetal Lung	lung
44	chr2:86682400-86702000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:86682400-86704000	Weak transcription	Stomach Mucosa	stomach
46	chr2:86683000-86709600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr2:86683400-86697800	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr2:86683400-86698200	Strong transcription	K562	blood
49	chr2:86683600-86695400	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr2:86683800-86694000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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