Variant report

Variant	rs2940745
Chromosome Location	chr15:49424665-49424666
allele	A/G
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	POLR2A	chr15:49424176-49425089	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49423792..49428339-chr15:49429632..49433589,5	K562	blood:

Variant related genes	Relation type
COPS2	TF binding region
ENSG00000166200	Chromatin interaction
ENSG00000200120	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10431775	0.81[ASN][1000 genomes]
rs1048975	0.96[ASN][1000 genomes]
rs10775139	0.88[ASN][1000 genomes]
rs11070682	0.81[ASN][1000 genomes]
rs11629547	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11632063	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11637991	0.82[ASN][1000 genomes]
rs11858114	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12440709	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12442679	0.89[ASN][1000 genomes]
rs12898691	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12902875	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2086256	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2127241	0.81[EUR][1000 genomes]
rs2127242	0.81[EUR][1000 genomes]
rs2127244	0.85[EUR][1000 genomes]
rs2169932	0.82[ASN][1000 genomes]
rs2219812	0.81[ASN][1000 genomes]
rs2263559	0.85[ASN][1000 genomes]
rs2413931	0.88[ASN][1000 genomes]
rs2413935	0.90[ASN][1000 genomes]
rs2413937	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2457228	0.86[ASN][1000 genomes]
rs2580923	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2580926	0.86[EUR][1000 genomes]
rs2663088	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2663089	0.88[ASN][1000 genomes]
rs2663090	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28437582	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28479967	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28539950	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28676698	0.86[ASN][1000 genomes]
rs28724568	0.81[ASN][1000 genomes]
rs28728368	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28731311	0.86[ASN][1000 genomes]
rs2899427	0.81[ASN][1000 genomes]
rs2899430	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2919148	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2940746	0.85[ASN][1000 genomes]
rs3098615	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3098620	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3105861	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3105863	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34854443	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4775804	0.85[EUR][1000 genomes]
rs4775805	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs490621	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs491277	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs500122	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55736202	0.86[ASN][1000 genomes]
rs563533	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs568726	0.86[ASN][1000 genomes]
rs600863	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs603868	0.90[ASN][1000 genomes]
rs62013266	0.82[ASN][1000 genomes]
rs626855	0.86[ASN][1000 genomes]
rs671945	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs679957	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs685172	0.86[ASN][1000 genomes]
rs7167338	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7167555	0.81[EUR][1000 genomes]
rs7176455	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2940745	GALK2	Cis_1M	lymphoblastoid	RTeQTL
rs2940745	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49388800-49434800	Weak transcription	Small Intestine	intestine
2	chr15:49395600-49426400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:49398600-49427600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:49403000-49434600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:49403400-49440200	Weak transcription	Pancreas	Pancrea
6	chr15:49403600-49432200	Weak transcription	Fetal Stomach	stomach
7	chr15:49403600-49435200	Weak transcription	Aorta	Aorta
8	chr15:49403600-49435200	Weak transcription	Gastric	stomach
9	chr15:49403600-49435400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:49403800-49433200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:49404800-49425600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:49404800-49434600	Weak transcription	Right Ventricle	heart
13	chr15:49404800-49435000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:49405600-49441800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:49411400-49432200	Weak transcription	Fetal Intestine Small	intestine
16	chr15:49413000-49427200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:49413400-49426200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:49413600-49447000	Weak transcription	Stomach Mucosa	stomach
19	chr15:49414000-49426400	Strong transcription	HSMM	muscle
20	chr15:49415200-49433400	Weak transcription	Lung	lung
21	chr15:49415400-49427400	Strong transcription	Hela-S3	cervix
22	chr15:49415400-49427600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:49415600-49427400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:49415600-49437600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr15:49415800-49437400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:49416200-49427600	Weak transcription	Fetal Brain Male	brain
27	chr15:49416200-49437400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:49416400-49427800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:49416800-49436800	Strong transcription	Liver	Liver
30	chr15:49416800-49437200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:49417000-49437200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:49417200-49424800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:49417200-49426600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:49417200-49436600	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr15:49417200-49437200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr15:49417200-49437200	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr15:49417200-49437400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr15:49417200-49437400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr15:49417400-49427600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr15:49417400-49427600	Strong transcription	Placenta	Placenta
41	chr15:49417400-49437200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr15:49417600-49437200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr15:49417600-49437200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr15:49417800-49437200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr15:49418000-49426200	Strong transcription	HUVEC	blood vessel
46	chr15:49418000-49435800	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr15:49418600-49426800	Strong transcription	Osteobl	bone
48	chr15:49418600-49436000	Strong transcription	Fetal Thymus	thymus
49	chr15:49418600-49437600	Strong transcription	Primary B cells from peripheral blood	blood
50	chr15:49418800-49426200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links