Variant report

Variant	rs17027169
Chromosome Location	chr2:86595833-86595834
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:86525475..86526402-chr2:86594830..86595950,4	MCF-7	breast:
2	chr17:79194432..79194952-chr2:86595492..86596036,3	K562	blood:
3	chr2:86448891..86450074-chr2:86594892..86595864,3	MCF-7	breast:
4	chr2:86446503..86449677-chr2:86593387..86596210,3	MCF-7	breast:
5	chr2:86447923..86448691-chr2:86595098..86596037,5	MCF-7	breast:
6	chr2:86420778..86424048-chr2:86595325..86598515,3	MCF-7	breast:
7	chr2:86525581..86526450-chr2:86595097..86596076,7	MCF-7	breast:
8	chr2:86572451..86574129-chr2:86595066..86597224,2	K562	blood:
9	chr2:86594067..86596122-chr2:86600316..86602892,2	MCF-7	breast:
10	chr2:86593659..86596612-chr2:86598158..86600807,3	K562	blood:
11	chr2:86421063..86423710-chr2:86595515..86598426,3	MCF-7	breast:
12	chr2:86588403..86590513-chr2:86593464..86596116,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000132305	Chromatin interaction
ENSG00000273080	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13405197	1.00[CEU][hapmap]
rs17027163	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55896146	0.88[EUR][1000 genomes]
rs56194753	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56233501	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61629709	0.88[EUR][1000 genomes]
rs6728272	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72926457	0.88[EUR][1000 genomes]
rs72926466	0.88[EUR][1000 genomes]
rs72926475	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17027169	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86593000-86596000	Enhancers	Fetal Intestine Small	intestine
2	chr2:86593400-86596000	Enhancers	Fetal Intestine Large	intestine
3	chr2:86593400-86596000	Enhancers	Pancreas	Pancrea
4	chr2:86594000-86596000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:86594000-86596000	Enhancers	Right Ventricle	heart
6	chr2:86594200-86596000	Enhancers	Primary hematopoietic stem cells	blood
7	chr2:86594200-86596000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:86594200-86596000	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr2:86594400-86596200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr2:86594600-86596000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr2:86594800-86596000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:86594800-86596000	Enhancers	Stomach Mucosa	stomach
13	chr2:86595000-86596000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:86595000-86596000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr2:86595000-86596200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:86595000-86596200	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr2:86595000-86596600	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr2:86595200-86596000	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr2:86595200-86596000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:86595200-86596000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:86595200-86596000	Enhancers	Brain Cingulate Gyrus	brain
22	chr2:86595200-86596000	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr2:86595200-86596000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:86595200-86596000	Enhancers	Fetal Heart	heart
25	chr2:86595200-86596000	Enhancers	Fetal Lung	lung
26	chr2:86595200-86596000	Enhancers	Fetal Thymus	thymus
27	chr2:86595200-86596000	Active TSS	Rectal Smooth Muscle	rectum
28	chr2:86595200-86596000	Enhancers	A549	lung
29	chr2:86595200-86596000	Flanking Active TSS	Hela-S3	cervix
30	chr2:86595200-86596000	Flanking Active TSS	HSMM	muscle
31	chr2:86595200-86596200	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr2:86595400-86596000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:86595400-86596000	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr2:86595400-86596000	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr2:86595400-86596000	Enhancers	Primary B cells from peripheral blood	blood
36	chr2:86595400-86596000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr2:86595400-86596000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:86595400-86596000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:86595400-86596000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:86595400-86596000	Enhancers	Esophagus	oesophagus
41	chr2:86595400-86596000	Enhancers	Fetal Brain Male	brain
42	chr2:86595400-86596000	Enhancers	Fetal Muscle Leg	muscle
43	chr2:86595400-86596000	Enhancers	Placenta	Placenta
44	chr2:86595400-86596000	Enhancers	Left Ventricle	heart
45	chr2:86595400-86596000	Enhancers	Ovary	ovary
46	chr2:86595400-86596000	Flanking Active TSS	HepG2	liver
47	chr2:86595400-86596200	Enhancers	Primary B cells from cord blood	blood
48	chr2:86595600-86596000	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr2:86595600-86596000	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr2:86595600-86596000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell

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