Variant report

Variant	rs56304923
Chromosome Location	chr2:86846399-86846400
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	chr2:86819094..86820925-chr2:86844374..86847111,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12464501	0.89[ASN][1000 genomes]
rs12468191	0.96[ASN][1000 genomes]
rs12471953	0.94[ASN][1000 genomes]
rs2044231	0.89[ASN][1000 genomes]
rs2044232	0.89[ASN][1000 genomes]
rs55708554	0.94[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	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	nsv1011590	chr2:86824181-86906114	Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56304923	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86825400-86849000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:86826800-86847800	Weak transcription	NHEK	skin
3	chr2:86828200-86847800	Weak transcription	NHLF	lung
4	chr2:86829400-86848400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:86829400-86849600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:86829800-86849400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:86830000-86848600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:86830400-86847600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr2:86830400-86848600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:86830600-86847000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:86830800-86847600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:86830800-86847800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:86830800-86848000	Strong transcription	Placenta	Placenta
14	chr2:86831000-86847200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:86831800-86848000	Weak transcription	HMEC	breast
16	chr2:86831800-86848200	Weak transcription	K562	blood
17	chr2:86832200-86848200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:86832400-86849400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:86832600-86848200	Weak transcription	Colonic Mucosa	Colon
20	chr2:86833000-86848200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:86834000-86846800	Strong transcription	Fetal Lung	lung
22	chr2:86834400-86846600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr2:86834400-86847000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:86834600-86847400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:86834600-86847800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr2:86835200-86847200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:86835200-86847800	Weak transcription	Hela-S3	cervix
28	chr2:86835400-86846600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:86835800-86847200	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr2:86835800-86847600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:86836600-86848600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:86837000-86848400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:86837200-86847800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:86838000-86846800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:86839000-86847400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:86839400-86847400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:86839600-86847600	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr2:86840000-86847200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:86840200-86846600	Strong transcription	Fetal Kidney	kidney
40	chr2:86840200-86847400	Strong transcription	Primary hematopoietic stem cells	blood
41	chr2:86840400-86847000	Strong transcription	Adipose Nuclei	Adipose
42	chr2:86840800-86846400	Strong transcription	Primary T cells from cord blood	blood
43	chr2:86840800-86847400	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr2:86840800-86847600	Strong transcription	HSMM	muscle
45	chr2:86841000-86847200	Weak transcription	Right Atrium	heart
46	chr2:86841000-86847600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:86841200-86847400	Weak transcription	Fetal Heart	heart
48	chr2:86841200-86847800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:86841200-86849600	Weak transcription	Gastric	stomach
50	chr2:86841200-86849600	Weak transcription	Spleen	Spleen

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