Variant report

Variant	rs1952607
Chromosome Location	chr13:30888981-30888982
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:30888078..30890627-chr13:31190542..31192551,3	MCF-7	breast:
2	chr13:30878723..30884002-chr13:30884417..30889770,9	K562	blood:
3	chr13:30874478..30877228-chr13:30887238..30890172,2	K562	blood:
4	chr13:30884908..30886563-chr13:30886759..30889976,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132952	Chromatin interaction
ENSG00000189403	Chromatin interaction
ENSG00000102781	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12874839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1296549	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs185694	0.90[CEU][hapmap];0.80[GIH][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs200505	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs200506	0.80[EUR][1000 genomes]
rs200512	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs202079	0.85[CEU][hapmap]
rs202098	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs202099	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs202101	0.89[CEU][hapmap]
rs595449	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs613291	0.85[CEU][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs628483	0.80[MEX][hapmap]
rs653251	0.85[CEU][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs672233	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs846495	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs846498	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9315003	0.94[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9506288	0.84[YRI][hapmap]
rs9506290	1.00[YRI][hapmap]
rs9508701	1.00[YRI][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1952607	C13orf26	cis	cerebellum	SCAN
rs1952607	KATNAL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30882000-30889000	Weak transcription	Spleen	Spleen
2	chr13:30882200-30889200	Weak transcription	Left Ventricle	heart
3	chr13:30882200-30889600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr13:30882200-30892200	Weak transcription	Psoas Muscle	Psoas
5	chr13:30882200-30893800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:30882200-30896200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr13:30882200-30896200	Weak transcription	Ovary	ovary
8	chr13:30882200-30910800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr13:30882400-30892000	Weak transcription	Fetal Muscle Leg	muscle
10	chr13:30882400-30892200	Weak transcription	Right Atrium	heart
11	chr13:30882400-30894800	Weak transcription	Fetal Intestine Small	intestine
12	chr13:30882400-30905400	Weak transcription	Right Ventricle	heart
13	chr13:30882400-30905400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr13:30883000-30889000	Weak transcription	Brain Anterior Caudate	brain
15	chr13:30883000-30889400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr13:30883000-30890400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr13:30884600-30896000	Enhancers	Fetal Heart	heart
18	chr13:30885000-30894600	Weak transcription	Aorta	Aorta
19	chr13:30885800-30889000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr13:30885800-30889800	Enhancers	Primary B cells from peripheral blood	blood
21	chr13:30885800-30889800	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr13:30886000-30898400	Weak transcription	Lung	lung
23	chr13:30886200-30889200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr13:30886200-30892000	Weak transcription	Dnd41	blood
25	chr13:30886400-30889200	Enhancers	NHLF	lung
26	chr13:30886800-30896800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr13:30886800-30900000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr13:30887000-30889400	Enhancers	Primary B cells from cord blood	blood
29	chr13:30887000-30889600	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr13:30887200-30889800	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr13:30887400-30889200	Enhancers	Primary T cells from cord blood	blood
32	chr13:30887400-30889600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr13:30887400-30889600	Enhancers	GM12878-XiMat	blood
34	chr13:30887600-30889200	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr13:30887600-30889800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr13:30887600-30890400	Weak transcription	Liver	Liver
37	chr13:30887600-30890400	Weak transcription	Brain Substantia Nigra	brain
38	chr13:30887600-30892600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr13:30887600-30893200	Weak transcription	NHDF-Ad	bronchial
40	chr13:30887600-30893400	Weak transcription	Brain Angular Gyrus	brain
41	chr13:30887800-30889000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr13:30887800-30891400	Weak transcription	Fetal Stomach	stomach
43	chr13:30887800-30892000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr13:30887800-30892000	Weak transcription	Adipose Nuclei	Adipose
45	chr13:30887800-30892000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr13:30887800-30892400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr13:30888000-30889000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr13:30888000-30889000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr13:30888000-30889600	Enhancers	Primary hematopoietic stem cells	blood
50	chr13:30888000-30889600	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links