Variant report

Variant	rs2254879
Chromosome Location	chr2:183991266-183991267
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:183775532..183777640-chr2:183990491..183993127,2	K562	blood:
2	chr2:183977949..183985615-chr2:183986503..183991971,13	K562	blood:
3	chr2:183895298..183904606-chr2:183986062..183992067,16	K562	blood:
4	chr2:183897885..183903273-chr2:183986817..183992325,13	K562	blood:
5	chr2:183989126..183990874-chr2:183990952..183992681,2	MCF-7	breast:
6	chr2:183990685..183993122-chr2:184003291..184005876,2	K562	blood:
7	chr2:183836718..183838459-chr2:183989290..183991920,2	K562	blood:
8	chr2:183954410..183956747-chr2:183990297..183991914,2	K562	blood:
9	chr2:183942911..183945636-chr2:183991182..183993608,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163002	Chromatin interaction
ENSG00000061676	Chromatin interaction
ENSG00000162999	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10497620	0.82[YRI][hapmap]
rs2675104	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2675105	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4666890	0.82[YRI][hapmap]
rs7577407	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv875485	chr2:183827018-184195265	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1010799	chr2:183855680-184244721	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv536072	chr2:183855680-184244721	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1003519	chr2:183885544-184015868	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv2763287	chr2:183939173-184037893	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2254879	C1QBP	trans	parietal	SCAN
rs2254879	SAP30BP	trans	parietal	SCAN
rs2254879	USP22	trans	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183988400-183991600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr2:183988800-183991600	Active TSS	K562	blood
3	chr2:183990000-183996200	Weak transcription	Lung	lung
4	chr2:183990000-184003600	Weak transcription	Left Ventricle	heart
5	chr2:183990000-184008600	Weak transcription	Esophagus	oesophagus
6	chr2:183990000-184008800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:183990000-184024400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:183990000-184050000	Weak transcription	Aorta	Aorta
9	chr2:183990200-183991400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr2:183990200-183991400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr2:183990200-183991600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:183990200-183993600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr2:183990200-183995000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:183990200-184008200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:183990200-184014200	Weak transcription	HSMMtube	muscle
16	chr2:183990200-184018800	Weak transcription	Placenta	Placenta
17	chr2:183990200-184036400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:183990400-183991400	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr2:183990400-183991400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:183990400-183991400	Flanking Active TSS	HMEC	breast
21	chr2:183990400-183991600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:183990400-183991600	Flanking Active TSS	HepG2	liver
23	chr2:183990400-183991800	Flanking Active TSS	A549	lung
24	chr2:183990400-183991800	Flanking Active TSS	Dnd41	blood
25	chr2:183990600-183992600	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr2:183990600-183994400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:183990600-183995400	Weak transcription	Colon Smooth Muscle	Colon
28	chr2:183990600-183995600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:183990600-183995800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:183990600-184010200	Weak transcription	Brain Substantia Nigra	brain
31	chr2:183990600-184028600	Weak transcription	Colonic Mucosa	Colon
32	chr2:183990800-183991400	Enhancers	Primary T cells from cord blood	blood
33	chr2:183990800-183991400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr2:183990800-183991400	Enhancers	HUVEC	blood vessel
35	chr2:183990800-183991600	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr2:183990800-183991600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:183990800-183991600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr2:183990800-183991600	Enhancers	Fetal Lung	lung
39	chr2:183990800-183993000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr2:183990800-183994400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:183990800-183994400	Weak transcription	Primary B cells from cord blood	blood
42	chr2:183990800-183995600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:183990800-184000000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr2:183990800-184025800	Weak transcription	Fetal Kidney	kidney
45	chr2:183990800-184031000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:183991000-183991400	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr2:183991000-183991400	Enhancers	NHDF-Ad	bronchial
48	chr2:183991000-183991400	Enhancers	NHLF	lung
49	chr2:183991000-183991600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr2:183991000-183991600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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