Variant report

Variant	rs28481675
Chromosome Location	chr17:46320031-46320032
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46297106..46299092-chr17:46317071..46320031,2	K562	blood:
2	chr17:46319745..46321628-chr17:46703138..46705535,2	K562	blood:
3	chr17:46312728..46315303-chr17:46319981..46321510,2	MCF-7	breast:
4	chr17:46312738..46316050-chr17:46317088..46320426,4	K562	blood:
5	chr17:46316932..46321831-chr17:46322420..46326261,9	K562	blood:
6	chr17:46297106..46299092-chr17:46317071..46320404,3	K562	blood:

Variant related genes	Relation type
ENSG00000170689	Chromatin interaction

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

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

rs_ID	r²[population]
rs11079810	0.86[EUR][1000 genomes]
rs11079813	0.87[EUR][1000 genomes]
rs11650476	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11654292	0.81[EUR][1000 genomes]
rs1544597	0.90[EUR][1000 genomes]
rs1975703	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56258199	0.81[EUR][1000 genomes]
rs60707285	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60843764	0.81[EUR][1000 genomes]
rs6504067	0.90[EUR][1000 genomes]
rs6504114	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6504115	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7207553	0.87[EUR][1000 genomes]
rs7210671	0.87[EUR][1000 genomes]
rs7220398	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7221897	0.87[EUR][1000 genomes]
rs7222646	0.81[EUR][1000 genomes]
rs7224155	0.87[EUR][1000 genomes]
rs7225288	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73322881	0.86[EUR][1000 genomes]
rs73322886	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs73324779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8071697	0.90[EUR][1000 genomes]
rs9890850	0.81[EUR][1000 genomes]
rs9893110	0.87[EUR][1000 genomes]
rs9894076	0.86[EUR][1000 genomes]
rs9907268	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28481675	PNPO	Cis_1M	lymphoblastoid	RTeQTL
rs28481675	RP5-890E16.2	cis	Nerve Tibial	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46306600-46335400	Weak transcription	Thymus	Thymus
2	chr17:46314200-46320200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr17:46315800-46323000	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr17:46316400-46322800	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr17:46316400-46324600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr17:46316600-46320200	Enhancers	Fetal Kidney	kidney
7	chr17:46316600-46320600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr17:46317200-46320200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr17:46317200-46322600	Enhancers	Fetal Intestine Small	intestine
10	chr17:46317200-46324000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr17:46317400-46322400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr17:46317400-46322800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr17:46317400-46322800	Enhancers	Fetal Intestine Large	intestine
14	chr17:46317600-46320400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr17:46317800-46320200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr17:46317800-46320600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr17:46317800-46323000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr17:46318800-46321400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr17:46318800-46321600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr17:46318800-46322400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr17:46318800-46322600	Enhancers	NHDF-Ad	bronchial
22	chr17:46319000-46321400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr17:46319000-46321400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr17:46319000-46321400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr17:46319000-46321400	Enhancers	A549	lung
26	chr17:46319000-46321400	Enhancers	K562	blood
27	chr17:46319000-46321600	Weak transcription	Hela-S3	cervix
28	chr17:46319000-46322000	Weak transcription	HSMMtube	muscle
29	chr17:46319000-46322600	Enhancers	GM12878-XiMat	blood
30	chr17:46319000-46324800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr17:46319200-46321400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr17:46319400-46320400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr17:46319400-46321000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr17:46319400-46321400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr17:46319400-46321600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr17:46319600-46320400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr17:46319600-46320400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr17:46319600-46320800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr17:46319600-46321000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr17:46319600-46321000	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr17:46319600-46321400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr17:46319600-46321400	Weak transcription	Fetal Lung	lung
43	chr17:46319600-46321400	Weak transcription	HMEC	breast
44	chr17:46319600-46321400	Weak transcription	NH-A	brain
45	chr17:46319600-46321600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr17:46319600-46322800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr17:46319600-46372000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr17:46319800-46320200	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr17:46319800-46320800	Weak transcription	HSMM	muscle
50	chr17:46319800-46321000	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links