Variant report

Variant	rs2424528
Chromosome Location	chr20:23361613-23361614
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	chr20:23344681..23346860-chr20:23360081..23363046,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125812	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1056394	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11087428	0.85[EUR][1000 genomes]
rs11905630	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1419005	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1419006	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1419009	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1419010	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16985308	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1936013	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2000261	0.84[ASN][1000 genomes]
rs2051093	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2144381	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2224074	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236022	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2249943	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2251145	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2252824	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2275787	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2275788	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2281429	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2424530	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2424531	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2424532	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2424534	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2424535	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2424536	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2424537	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2424539	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2424540	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2424541	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2424544	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2424545	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2424546	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2424548	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2424549	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2424550	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2424551	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2424552	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2424554	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2424556	0.85[EUR][1000 genomes]
rs2424557	0.85[EUR][1000 genomes]
rs3746734	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4813490	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4813491	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4813493	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4813495	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4815199	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4815203	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6048778	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6076057	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6076059	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6076071	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6076073	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6083083	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6083084	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6083085	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6083087	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6083088	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6083092	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6083095	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6083099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083104	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6083105	0.81[AFR][1000 genomes]
rs6083110	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6083111	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6083119	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6114085	0.85[EUR][1000 genomes]
rs6132604	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6132607	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6132612	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6137899	0.87[ASN][1000 genomes]
rs6137905	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6137908	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6137909	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6137922	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6137924	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6137934	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6137940	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6137949	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7269627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743022	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs743023	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs743024	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs761726	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7988	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8118688	0.89[ASN][1000 genomes]
rs8183442	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2424528	NAPB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23344000-23392600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:23344800-23362400	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr20:23345000-23361800	Strong transcription	Fetal Thymus	thymus
4	chr20:23345000-23362000	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr20:23345000-23362600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr20:23346600-23363200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr20:23346800-23362600	Weak transcription	Right Atrium	heart
8	chr20:23347200-23362400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr20:23347400-23362000	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr20:23347800-23362000	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr20:23347800-23362200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr20:23347800-23362600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr20:23348000-23374200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr20:23348200-23384800	Weak transcription	Stomach Mucosa	stomach
15	chr20:23348400-23362000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr20:23348600-23362400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr20:23348600-23363000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr20:23348800-23362000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr20:23348800-23363000	Strong transcription	GM12878-XiMat	blood
20	chr20:23348800-23366400	Strong transcription	Dnd41	blood
21	chr20:23349200-23363000	Strong transcription	Adipose Nuclei	Adipose
22	chr20:23349400-23363200	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr20:23349600-23363600	Strong transcription	Liver	Liver
24	chr20:23349600-23366000	Strong transcription	HepG2	liver
25	chr20:23349800-23362000	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr20:23349800-23362800	Strong transcription	Osteobl	bone
27	chr20:23349800-23363000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr20:23349800-23364200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr20:23350000-23363000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr20:23350000-23363600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr20:23350400-23362600	Strong transcription	Placenta	Placenta
32	chr20:23351200-23371000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr20:23351200-23374000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr20:23351400-23374000	Weak transcription	Fetal Brain Male	brain
35	chr20:23352200-23367800	Weak transcription	Small Intestine	intestine
36	chr20:23352800-23362800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr20:23352800-23376400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr20:23353000-23365400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr20:23353000-23378200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr20:23353400-23372400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr20:23353400-23374200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr20:23354400-23389000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr20:23354400-23399800	Weak transcription	Hela-S3	cervix
44	chr20:23354600-23374200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr20:23354600-23375200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr20:23354800-23362800	Weak transcription	Spleen	Spleen
47	chr20:23354800-23371000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr20:23354800-23373600	Weak transcription	Colonic Mucosa	Colon
49	chr20:23356200-23362000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr20:23356400-23362000	Strong transcription	Brain Inferior Temporal Lobe	brain

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