Variant report

Variant	rs17767270
Chromosome Location	chr15:42898612-42898613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42896121..42899358-chr15:42903521..42907141,3	K562	blood:
2	chr15:42890368..42894059-chr15:42896561..42900467,4	K562	blood:
3	chr15:42896121..42899358-chr15:42902188..42907141,4	K562	blood:
4	chr15:42898237..42899774-chr15:42911395..42914292,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10454692	0.83[EUR][1000 genomes]
rs1048571	0.82[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs11070375	0.95[EUR][1000 genomes]
rs11630625	0.80[AMR][1000 genomes]
rs11630681	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11635076	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11635889	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs11636209	0.82[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs12438021	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12439377	0.82[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs12440118	1.00[MEX][hapmap];0.81[TSI][hapmap]
rs12440506	0.83[EUR][1000 genomes]
rs12910538	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12914539	1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17709867	1.00[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17766258	0.82[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs17767264	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41315252	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56172155	0.98[EUR][1000 genomes]
rs62019280	0.81[EUR][1000 genomes]
rs62019282	0.81[EUR][1000 genomes]
rs62019285	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62019287	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62019294	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62019312	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62019315	0.83[EUR][1000 genomes]
rs62019320	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019322	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7182376	0.83[EUR][1000 genomes]
rs72711767	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73406562	0.81[AFR][1000 genomes]
rs8039240	0.81[EUR][1000 genomes]
rs8042618	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17767270	CEP27	Cis_1M	lymphoblastoid	RTeQTL
rs17767270	SNAP23	cis	parietal	SCAN
rs17767270	TUBGCP4	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42874400-42900200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:42874400-42900200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr15:42874400-42900200	Weak transcription	Lung	lung
4	chr15:42874800-42929800	Weak transcription	Fetal Brain Female	brain
5	chr15:42876800-42900200	Weak transcription	HMEC	breast
6	chr15:42877000-42900200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:42877200-42911200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr15:42888600-42901200	Weak transcription	Fetal Brain Male	brain
9	chr15:42888800-42901000	Weak transcription	Brain Angular Gyrus	brain
10	chr15:42888800-42909600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr15:42888800-42911000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:42889600-42903600	Weak transcription	Ovary	ovary
13	chr15:42895000-42911800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:42895200-42900000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr15:42895200-42914200	Weak transcription	HepG2	liver
16	chr15:42895200-42920800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:42896200-42898800	Enhancers	Fetal Stomach	stomach
18	chr15:42896200-42901600	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr15:42896400-42901600	Enhancers	Fetal Heart	heart
20	chr15:42896600-42898800	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr15:42896600-42898800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr15:42896800-42901800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr15:42896800-42902000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:42897000-42899200	Enhancers	Left Ventricle	heart
25	chr15:42897000-42899400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr15:42897000-42901800	Enhancers	Primary B cells from peripheral blood	blood
27	chr15:42897200-42898800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:42897400-42898800	Enhancers	Aorta	Aorta
29	chr15:42897400-42899200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr15:42897600-42900200	Weak transcription	NH-A	brain
31	chr15:42897800-42898800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:42897800-42899000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr15:42897800-42900600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:42897800-42900600	Enhancers	Primary hematopoietic stem cells	blood
35	chr15:42897800-42903800	Weak transcription	Psoas Muscle	Psoas
36	chr15:42897800-42914600	Weak transcription	Brain Germinal Matrix	brain
37	chr15:42897800-42930200	Weak transcription	HSMM	muscle
38	chr15:42898000-42899000	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr15:42898000-42899000	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr15:42898000-42899400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr15:42898000-42899400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr15:42898000-42900000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr15:42898000-42900000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr15:42898000-42900000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:42898000-42900200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:42898000-42900200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:42898000-42900200	Weak transcription	Placenta	Placenta
48	chr15:42898000-42900200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr15:42898000-42900200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr15:42898000-42900200	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links