Variant report

Variant	rs2424544
Chromosome Location	chr20:23390314-23390315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23383896..23386214-chr20:23390007..23393764,3	MCF-7	breast:
2	chr20:23388261..23390849-chr20:23399031..23401935,2	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1056394	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11087428	0.87[EUR][1000 genomes]
rs11905630	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1419005	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1419006	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1419009	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1419010	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16985308	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1936013	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2051093	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2144381	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2224074	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2236022	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2249943	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252824	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2275787	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2275788	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2281429	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281430	0.81[AFR][1000 genomes]
rs2424528	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2424530	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2424531	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2424532	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2424533	0.83[AFR][1000 genomes]
rs2424534	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424535	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2424536	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424537	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424538	0.83[AFR][1000 genomes]
rs2424539	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424540	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2424541	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424546	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424547	0.86[AFR][1000 genomes]
rs2424548	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2424549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2424551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424552	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2424553	0.83[AFR][1000 genomes]
rs2424554	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2424556	0.87[EUR][1000 genomes]
rs2424557	0.87[EUR][1000 genomes]
rs3746734	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4813490	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4813491	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4813493	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4813495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815199	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4815203	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048778	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6076057	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6076059	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6076071	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6076073	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6083083	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6083084	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6083085	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6083087	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6083088	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6083092	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6083095	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6083099	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6083100	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6083104	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6083110	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6083111	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083119	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114085	0.87[EUR][1000 genomes]
rs6132604	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6132607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132612	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6137905	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6137908	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6137909	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6137922	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6137924	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6137934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6137949	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7269627	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs743022	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs743023	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs743024	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs761726	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7988	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8118688	0.82[ASN][1000 genomes]
rs8183442	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2424544	NAPB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23344000-23392600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:23354400-23399800	Weak transcription	Hela-S3	cervix
3	chr20:23361200-23399600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr20:23372800-23400800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr20:23375600-23390600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr20:23375600-23396800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr20:23375600-23400000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr20:23375800-23396200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr20:23375800-23400000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr20:23375800-23400200	Weak transcription	Fetal Brain Male	brain
11	chr20:23376000-23390400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr20:23376600-23400400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr20:23376800-23391800	Weak transcription	Adipose Nuclei	Adipose
14	chr20:23377000-23398400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr20:23378200-23391800	Weak transcription	Brain Angular Gyrus	brain
16	chr20:23378200-23400000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr20:23378400-23399800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr20:23378800-23390400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr20:23378800-23391800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr20:23378800-23396400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr20:23378800-23399800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr20:23379000-23400000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr20:23379000-23400200	Weak transcription	Primary B cells from cord blood	blood
24	chr20:23379000-23400400	Weak transcription	Brain Substantia Nigra	brain
25	chr20:23379200-23392600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr20:23379200-23400000	Weak transcription	HUVEC	blood vessel
27	chr20:23379200-23400200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr20:23380800-23400000	Weak transcription	NH-A	brain
29	chr20:23382000-23391000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr20:23382000-23400200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr20:23382200-23390600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr20:23382200-23390800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr20:23382200-23391800	Weak transcription	HSMM	muscle
34	chr20:23382200-23398400	Weak transcription	Fetal Brain Female	brain
35	chr20:23382200-23400200	Weak transcription	A549	lung
36	chr20:23382400-23392800	Weak transcription	Pancreas	Pancrea
37	chr20:23382400-23397400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr20:23383000-23390400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr20:23383000-23398000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr20:23383000-23399800	Weak transcription	Fetal Intestine Small	intestine
41	chr20:23383000-23400400	Weak transcription	Thymus	Thymus
42	chr20:23383200-23391200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr20:23383200-23392000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr20:23383200-23400000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr20:23383600-23390400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr20:23383600-23390600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr20:23383600-23392600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr20:23383600-23395800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr20:23383600-23396000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr20:23383600-23396400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links