Variant report

Variant	rs13005269
Chromosome Location	chr2:86563739-86563740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86422237..86423747-chr2:86562559..86564958,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273080	Chromatin interaction
ENSG00000132305	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12471787	0.85[AMR][1000 genomes]
rs12714181	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4430958	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs766285	0.89[AMR][1000 genomes];0.82[ASN][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	esv3357801	chr2:86563266-86566214	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv3448068	chr2:86563641-86565889	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13005269	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86552200-86563800	Weak transcription	Aorta	Aorta
2	chr2:86562400-86565000	Active TSS	Fetal Brain Female	brain
3	chr2:86563000-86563800	Bivalent Enhancer	Stomach Mucosa	stomach
4	chr2:86563000-86564000	Flanking Active TSS	Brain Germinal Matrix	brain
5	chr2:86563000-86564000	Flanking Active TSS	Fetal Brain Male	brain
6	chr2:86563000-86564000	Bivalent Enhancer	Placenta	Placenta
7	chr2:86563000-86564000	Flanking Active TSS	Pancreas	Pancrea
8	chr2:86563000-86564000	Flanking Active TSS	Right Ventricle	heart
9	chr2:86563000-86564200	Flanking Active TSS	Colon Smooth Muscle	Colon
10	chr2:86563000-86564200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
11	chr2:86563000-86564200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
12	chr2:86563000-86564200	Flanking Active TSS	Hela-S3	cervix
13	chr2:86563000-86565200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
14	chr2:86563000-86565600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr2:86563200-86563800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:86563200-86563800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:86563200-86563800	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:86563200-86563800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:86563200-86563800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:86563200-86563800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:86563200-86563800	Flanking Active TSS	Fetal Heart	heart
22	chr2:86563200-86563800	Bivalent Enhancer	Fetal Lung	lung
23	chr2:86563200-86563800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
24	chr2:86563200-86563800	Bivalent Enhancer	A549	lung
25	chr2:86563200-86563800	Bivalent Enhancer	NHEK	skin
26	chr2:86563200-86564000	Bivalent Enhancer	Liver	Liver
27	chr2:86563200-86564000	Flanking Active TSS	Brain Angular Gyrus	brain
28	chr2:86563200-86564000	Bivalent Enhancer	Esophagus	oesophagus
29	chr2:86563200-86564000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
30	chr2:86563200-86564000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
31	chr2:86563200-86564000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
32	chr2:86563200-86564000	Enhancers	Spleen	Spleen
33	chr2:86563200-86564200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:86563200-86564200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr2:86563200-86564200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
36	chr2:86563200-86564400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:86563200-86564400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:86563200-86565000	Active TSS	Brain Anterior Caudate	brain
39	chr2:86563400-86563800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
40	chr2:86563400-86563800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
41	chr2:86563400-86563800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:86563400-86563800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:86563400-86563800	Bivalent Enhancer	Colonic Mucosa	Colon
44	chr2:86563400-86563800	Bivalent/Poised TSS	Fetal Stomach	stomach
45	chr2:86563400-86563800	Enhancers	Gastric	stomach
46	chr2:86563400-86563800	Flanking Active TSS	Left Ventricle	heart
47	chr2:86563400-86563800	Flanking Active TSS	HSMMtube	muscle
48	chr2:86563400-86564000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr2:86563400-86564200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:86563400-86564200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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