Variant report

Variant	rs2413926
Chromosome Location	chr15:49336477-49336478
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr15:49336274-49339327	Hela-S3	cervix:	n/a	n/a
2	CUX1	chr15:49336189-49336504	GM12878	blood:	n/a	n/a
3	CEBPB	chr15:49336425-49336482	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49335254..49337373-chr15:49461305..49463777,2	MCF-7	breast:

Variant related genes	Relation type
RN7SL577P	TF binding region
ENSG00000264210	Chromatin interaction
ENSG00000156958	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11070673	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11858814	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs12900819	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12901353	0.80[CEU][hapmap]
rs12905094	0.85[CEU][hapmap]
rs17435932	0.84[CEU][hapmap]
rs17472989	0.85[CEU][hapmap]
rs2289389	0.85[CEU][hapmap]
rs34748066	0.84[CEU][hapmap]
rs4775794	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7164309	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8043493	0.84[CEU][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2413926	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49283600-49337600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:49320200-49336800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr15:49321400-49338000	Weak transcription	Spleen	Spleen
4	chr15:49321800-49336800	Weak transcription	Thymus	Thymus
5	chr15:49327800-49337200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:49328400-49336600	Weak transcription	Aorta	Aorta
7	chr15:49328400-49336600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr15:49328400-49338000	Weak transcription	Esophagus	oesophagus
9	chr15:49328600-49337400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:49328600-49337400	Weak transcription	Colonic Mucosa	Colon
11	chr15:49328600-49337400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr15:49328600-49338000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:49328600-49338000	Weak transcription	Gastric	stomach
14	chr15:49329200-49336600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:49329200-49336600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr15:49329200-49337400	Weak transcription	Fetal Muscle Leg	muscle
17	chr15:49329200-49337400	Weak transcription	Fetal Thymus	thymus
18	chr15:49329400-49336600	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr15:49330000-49336600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr15:49331200-49336600	Weak transcription	Stomach Mucosa	stomach
21	chr15:49333600-49336600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr15:49333800-49337200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr15:49334000-49336600	Weak transcription	Fetal Kidney	kidney
24	chr15:49334600-49336600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr15:49334800-49336600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:49334800-49337000	Weak transcription	HSMM	muscle
27	chr15:49334800-49337800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:49335000-49336600	Weak transcription	Small Intestine	intestine
29	chr15:49335200-49336600	Weak transcription	Ovary	ovary
30	chr15:49335200-49336600	Weak transcription	Psoas Muscle	Psoas
31	chr15:49335200-49337400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr15:49335200-49337400	Weak transcription	Left Ventricle	heart
33	chr15:49335200-49337600	Weak transcription	Lung	lung
34	chr15:49335200-49337600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr15:49335200-49337800	Weak transcription	Pancreas	Pancrea
36	chr15:49335200-49338000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:49335400-49337200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr15:49335400-49337400	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr15:49335600-49336600	Enhancers	Liver	Liver
40	chr15:49335600-49336600	Enhancers	Hela-S3	cervix
41	chr15:49335600-49337200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:49335600-49337200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr15:49335800-49336600	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr15:49335800-49336600	Enhancers	Primary T cells from cord blood	blood
45	chr15:49335800-49336600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:49335800-49337200	Enhancers	Primary B cells from cord blood	blood
47	chr15:49335800-49337200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:49335800-49337400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:49335800-49337600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr15:49335800-49339200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links