Variant report

Variant	rs4832041
Chromosome Location	chr2:86776466-86776467
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1015117	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10184879	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10187880	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1020306	0.83[EUR][1000 genomes]
rs11127045	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11127046	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1137684	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11676576	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11684230	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11689330	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12328637	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12613282	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12614447	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12615285	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12714188	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12987172	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12991654	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13015620	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13034615	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13390713	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13408041	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13429696	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1465813	0.81[AMR][1000 genomes]
rs1518807	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2241803	0.81[AMR][1000 genomes]
rs3201448	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3731812	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4832040	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4832042	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4832297	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4832299	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4832300	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4832304	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62147239	0.81[EUR][1000 genomes]
rs6728211	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6738663	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6750226	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7369138	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7601115	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9284788	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv829488	chr2:86769108-86780946	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4832041	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86734000-86784800	Weak transcription	Osteobl	bone
2	chr2:86737400-86788400	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:86737800-86779600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr2:86753800-86788400	Weak transcription	HSMM	muscle
5	chr2:86756000-86788400	Weak transcription	Brain Anterior Caudate	brain
6	chr2:86756600-86779000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:86756600-86779000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:86756600-86784800	Weak transcription	Left Ventricle	heart
9	chr2:86756600-86789200	Weak transcription	Aorta	Aorta
10	chr2:86756800-86779400	Weak transcription	NHDF-Ad	bronchial
11	chr2:86761200-86788600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:86761200-86788800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:86761400-86779400	Weak transcription	NHEK	skin
14	chr2:86764600-86779600	Weak transcription	HMEC	breast
15	chr2:86768200-86785000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:86768800-86780000	Weak transcription	Small Intestine	intestine
17	chr2:86768800-86784200	Weak transcription	Psoas Muscle	Psoas
18	chr2:86768800-86785200	Weak transcription	Stomach Mucosa	stomach
19	chr2:86769400-86785600	Weak transcription	Fetal Heart	heart
20	chr2:86770000-86779000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:86771000-86777600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
22	chr2:86771200-86788400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:86771400-86779000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr2:86771400-86786200	Weak transcription	HSMMtube	muscle
25	chr2:86772200-86779000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:86772600-86777200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:86772800-86778200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:86773000-86776600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
29	chr2:86773000-86779000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:86773200-86781400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:86773400-86784200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:86773600-86779600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
33	chr2:86773800-86776600	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr2:86773800-86778000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
35	chr2:86774200-86788200	Weak transcription	Adipose Nuclei	Adipose
36	chr2:86774400-86777200	Weak transcription	Liver	Liver
37	chr2:86774400-86788800	Weak transcription	Fetal Lung	lung
38	chr2:86774600-86788200	Weak transcription	Hela-S3	cervix
39	chr2:86774800-86778600	Weak transcription	Primary B cells from cord blood	blood
40	chr2:86774800-86778600	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr2:86774800-86785200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:86775000-86779600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:86775200-86777200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr2:86775200-86782600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr2:86775200-86784200	Weak transcription	A549	lung
46	chr2:86775200-86784800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr2:86775200-86785200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:86775200-86788200	Weak transcription	K562	blood
49	chr2:86775200-86788800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr2:86775400-86777400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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