Variant report

Variant	rs2884005
Chromosome Location	chr2:172268061-172268062
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172265755..172268604-chr2:172378756..172380414,2	K562	blood:
2	chr2:172267543..172269824-chr2:172270765..172273272,4	K562	blood:
3	chr2:172267095..172269091-chr2:172287123..172288853,2	K562	blood:
4	chr2:172267840..172270296-chr2:172270765..172273449,2	K562	blood:
5	chr2:172265528..172268533-chr2:172288621..172291396,3	MCF-7	breast:
6	chr2:172265513..172268385-chr2:172270721..172272607,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123600	Chromatin interaction
ENSG00000115827	Chromatin interaction
ENSG00000071967	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs2193454	0.82[CHB][hapmap]

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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2884005	CDCA7	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172222200-172289600	Weak transcription	Gastric	stomach
2	chr2:172238000-172272400	Weak transcription	Fetal Intestine Large	intestine
3	chr2:172238800-172272400	Weak transcription	Primary T cells from cord blood	blood
4	chr2:172258600-172272400	Weak transcription	A549	lung
5	chr2:172259400-172272200	Weak transcription	Fetal Intestine Small	intestine
6	chr2:172260000-172271000	Weak transcription	K562	blood
7	chr2:172260200-172272200	Weak transcription	HepG2	liver
8	chr2:172261600-172277800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:172262400-172268800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:172264800-172272400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:172265000-172272200	Weak transcription	Primary B cells from cord blood	blood
12	chr2:172266000-172269800	Enhancers	NHDF-Ad	bronchial
13	chr2:172266400-172268200	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:172266400-172268600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:172266400-172268600	Weak transcription	Brain Angular Gyrus	brain
16	chr2:172266400-172268800	Enhancers	HSMM	muscle
17	chr2:172266400-172269000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr2:172266400-172269200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr2:172266400-172269400	Enhancers	HUVEC	blood vessel
20	chr2:172266400-172269600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:172266400-172269600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr2:172266400-172270000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:172266400-172271200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr2:172266400-172271600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr2:172266400-172272200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:172266400-172272200	Weak transcription	Brain Anterior Caudate	brain
27	chr2:172266400-172272400	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:172266400-172272400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:172266400-172277400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:172266400-172280400	Weak transcription	Esophagus	oesophagus
31	chr2:172266400-172280400	Weak transcription	Left Ventricle	heart
32	chr2:172266400-172289600	Weak transcription	Psoas Muscle	Psoas
33	chr2:172266400-172289600	Weak transcription	Right Ventricle	heart
34	chr2:172266600-172268800	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr2:172266600-172268800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:172266600-172269200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:172266600-172269200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:172266800-172269200	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr2:172266800-172272200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr2:172266800-172272200	Weak transcription	Fetal Stomach	stomach
41	chr2:172267000-172269000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:172267200-172268200	Enhancers	GM12878-XiMat	blood
43	chr2:172267200-172268600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:172267200-172268600	Weak transcription	HSMMtube	muscle
45	chr2:172267200-172269200	Enhancers	HMEC	breast
46	chr2:172267200-172269200	Enhancers	NHEK	skin
47	chr2:172267200-172269800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:172267400-172268200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:172267400-172268400	Weak transcription	Fetal Brain Female	brain
50	chr2:172267400-172268600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links