Variant report

Variant	rs4142246
Chromosome Location	chr20:23388975-23388976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23387020..23389665-chr20:23401490..23404499,3	MCF-7	breast:
2	chr20:23388261..23390849-chr20:23399031..23401935,2	K562	blood:
3	chr20:23341861..23344169-chr20:23387452..23389386,2	MCF-7	breast:
4	chr20:23384958..23386929-chr20:23388676..23390243,2	K562	blood:

Variant related genes	Relation type
ENSG00000125814	Chromatin interaction
ENSG00000125812	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1016628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12349	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1419007	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2024746	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2180139	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2236023	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2243448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2253834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2281431	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2295239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2424527	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2424542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2424555	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2424559	0.80[EUR][1000 genomes]
rs3746736	0.81[EUR][1000 genomes]
rs4815198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048750	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6048760	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6048779	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6048781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048784	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6076055	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6083114	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6083127	0.82[EUR][1000 genomes]
rs6137933	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs761723	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs999068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4142246	NAPB	cis	Skin Sun Exposed Lower leg	GTEx
rs4142246	NAPB	cis	Artery Tibial	GTEx

Chromatin state (count:104 , 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	chr20:23354400-23389000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr20:23354400-23399800	Weak transcription	Hela-S3	cervix
4	chr20:23361200-23399600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr20:23372800-23400800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:23375000-23389800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:23375600-23390600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr20:23375600-23396800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr20:23375600-23400000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr20:23375800-23396200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr20:23375800-23400000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr20:23375800-23400200	Weak transcription	Fetal Brain Male	brain
13	chr20:23376000-23389000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr20:23376000-23390400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr20:23376200-23389000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr20:23376600-23400400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr20:23376800-23391800	Weak transcription	Adipose Nuclei	Adipose
18	chr20:23377000-23398400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr20:23378200-23391800	Weak transcription	Brain Angular Gyrus	brain
20	chr20:23378200-23400000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr20:23378400-23399800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr20:23378800-23390400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr20:23378800-23391800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr20:23378800-23396400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr20:23378800-23399800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr20:23379000-23389600	Weak transcription	Brain Hippocampus Middle	brain
27	chr20:23379000-23400000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr20:23379000-23400200	Weak transcription	Primary B cells from cord blood	blood
29	chr20:23379000-23400400	Weak transcription	Brain Substantia Nigra	brain
30	chr20:23379200-23392600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr20:23379200-23400000	Weak transcription	HUVEC	blood vessel
32	chr20:23379200-23400200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr20:23380800-23400000	Weak transcription	NH-A	brain
34	chr20:23382000-23391000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr20:23382000-23400200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr20:23382200-23390600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr20:23382200-23390800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr20:23382200-23391800	Weak transcription	HSMM	muscle
39	chr20:23382200-23398400	Weak transcription	Fetal Brain Female	brain
40	chr20:23382200-23400200	Weak transcription	A549	lung
41	chr20:23382400-23392800	Weak transcription	Pancreas	Pancrea
42	chr20:23382400-23397400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr20:23383000-23390400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr20:23383000-23398000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr20:23383000-23399800	Weak transcription	Fetal Intestine Small	intestine
46	chr20:23383000-23400400	Weak transcription	Thymus	Thymus
47	chr20:23383200-23391200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr20:23383200-23392000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr20:23383200-23400000	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr20:23383600-23389000	Weak transcription	Primary T cells from cord blood	blood

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