Variant report

Variant	rs2424533
Chromosome Location	chr20:23375907-23375908
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	chr20:23375343..23377250-chr20:23393102..23394954,2	K562	blood:
2	chr20:23368241..23370501-chr20:23374374..23376749,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1003417	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1419008	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2144381	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2251145	0.83[AFR][1000 genomes]
rs2281430	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2405231	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2424529	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2424534	0.93[ASW][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2424535	0.85[AFR][1000 genomes]
rs2424537	0.85[AFR][1000 genomes]
rs2424538	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2424541	0.81[AFR][1000 genomes]
rs2424543	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2424544	0.83[AFR][1000 genomes]
rs2424545	0.93[ASW][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2424547	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2424549	0.83[AFR][1000 genomes]
rs2424550	0.83[AFR][1000 genomes]
rs2424551	0.83[AFR][1000 genomes]
rs2424553	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4813495	0.83[AFR][1000 genomes]
rs4815199	1.00[YRI][hapmap]
rs6048777	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6048778	0.86[ASW][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6048797	0.86[EUR][1000 genomes]
rs6076065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6083099	1.00[YRI][hapmap]
rs6083100	1.00[YRI][hapmap]
rs6083104	0.93[ASW][hapmap];1.00[YRI][hapmap]
rs6083105	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6083106	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6083111	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs6132607	0.93[ASW][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs6137934	0.83[AFR][1000 genomes]
rs6137940	0.83[AFR][1000 genomes]
rs743021	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs743024	0.93[ASW][hapmap];1.00[YRI][hapmap]
rs761723	0.81[CEU][hapmap]
rs761726	0.81[AFR][1000 genomes]
rs7988	0.86[ASW][hapmap]
rs999072	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2424533	NAPB	cis	Esophagus Muscularis	GTEx
rs2424533	NAPB	cis	Artery Tibial	GTEx
rs2424533	CST9L	cis	parietal	SCAN
rs2424533	GGTLC1	cis	cerebellum	SCAN

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	chr20:23348200-23384800	Weak transcription	Stomach Mucosa	stomach
3	chr20:23352800-23376400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr20:23353000-23378200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr20:23354400-23389000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr20:23354400-23399800	Weak transcription	Hela-S3	cervix
7	chr20:23358200-23377800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr20:23361200-23399600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr20:23364800-23378000	Strong transcription	Primary T cells from cord blood	blood
10	chr20:23365400-23376200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr20:23365800-23376000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr20:23366400-23377600	Weak transcription	Right Atrium	heart
13	chr20:23366800-23376200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr20:23366800-23382400	Strong transcription	Dnd41	blood
15	chr20:23367000-23377000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr20:23367000-23378200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr20:23367200-23376000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr20:23367200-23376000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr20:23367200-23377600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr20:23367600-23376400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr20:23367800-23376000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr20:23367800-23380400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr20:23368000-23376200	Strong transcription	Fetal Intestine Large	intestine
24	chr20:23368000-23376400	Strong transcription	Liver	Liver
25	chr20:23368200-23376200	Strong transcription	HepG2	liver
26	chr20:23368400-23376200	Strong transcription	Brain Anterior Caudate	brain
27	chr20:23368400-23376200	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr20:23368400-23376600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr20:23368400-23376800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr20:23368400-23376800	Strong transcription	Adipose Nuclei	Adipose
31	chr20:23368800-23376000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr20:23368800-23377000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr20:23369200-23376200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr20:23370000-23376200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr20:23370000-23377000	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr20:23370200-23376000	Strong transcription	Stomach Smooth Muscle	stomach
37	chr20:23370200-23376000	Strong transcription	HSMMtube	muscle
38	chr20:23370200-23376200	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr20:23370800-23377800	Weak transcription	NH-A	brain
40	chr20:23371000-23376000	Strong transcription	Aorta	Aorta
41	chr20:23371000-23376000	Strong transcription	Lung	lung
42	chr20:23371200-23376000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr20:23371600-23377000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr20:23372400-23376000	Strong transcription	Colon Smooth Muscle	Colon
45	chr20:23372400-23376200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr20:23372400-23378600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr20:23372600-23376000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr20:23372600-23376000	Strong transcription	Fetal Muscle Leg	muscle
49	chr20:23372600-23376000	Strong transcription	Placenta	Placenta
50	chr20:23372600-23376000	Strong transcription	Spleen	Spleen

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