Variant report

Variant	rs5960055
Chromosome Location	chrX:54954514-54954515
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:54948175..54950952-chrX:54954320..54957077,2	MCF-7	breast:
2	chrX:54917974..54918619-chrX:54953787..54954658,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PFKFB1-1	chrX:54954463-54956380	NONHSAT137236

Variant related genes	Relation type
ENSG00000067445	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1043031	0.94[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs1043034	0.94[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs1043044	0.94[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs12014660	0.89[CEU][hapmap];0.81[CHB][hapmap];0.97[TSI][hapmap]
rs12851962	1.00[CEU][hapmap];0.96[GIH][hapmap];0.97[TSI][hapmap]
rs12858090	0.94[CEU][hapmap];0.87[CHB][hapmap]
rs12858147	0.94[CEU][hapmap];0.87[CHB][hapmap]
rs2005463	0.89[CEU][hapmap];0.92[GIH][hapmap];0.94[TSI][hapmap]
rs2071932	0.94[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2071933	0.94[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2071934	0.94[CEU][hapmap];0.87[CHB][hapmap]
rs2273138	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs2281383	1.00[CEU][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap]
rs2361189	0.94[CEU][hapmap]
rs3765479	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs4826364	0.89[CEU][hapmap];0.80[CHD][hapmap];0.96[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap]
rs4826365	0.89[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.96[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap]
rs5914241	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs5960336	0.94[CEU][hapmap];0.86[CHB][hapmap]
rs6611391	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs704145	0.81[GIH][hapmap]
rs743974	0.94[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs763183	0.94[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs763184	0.94[CEU][hapmap];0.87[CHB][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5960055	TRO	cis	lymphoblastoid	seeQTL
rs5960055	TRO	cis	multi-tissue	Pritchard

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:54947800-54955400	Weak transcription	Spleen	Spleen
2	chrX:54948400-54954800	Weak transcription	Aorta	Aorta
3	chrX:54948400-54957800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chrX:54948400-54961800	Weak transcription	HSMMtube	muscle
5	chrX:54948400-54963000	Weak transcription	Gastric	stomach
6	chrX:54948600-54956400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chrX:54948600-54956800	Weak transcription	HSMM	muscle
8	chrX:54948600-54957800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chrX:54948600-54957800	Weak transcription	HepG2	liver
10	chrX:54948600-54959000	Weak transcription	Primary T cells from cord blood	blood
11	chrX:54948800-54955000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chrX:54948800-54955000	Weak transcription	Thymus	Thymus
13	chrX:54948800-54955200	Weak transcription	Brain Cingulate Gyrus	brain
14	chrX:54948800-54957000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chrX:54948800-54957400	Weak transcription	Right Atrium	heart
16	chrX:54948800-54957800	Weak transcription	Right Ventricle	heart
17	chrX:54948800-54957800	Weak transcription	Osteobl	bone
18	chrX:54948800-54958200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chrX:54948800-54958600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
20	chrX:54948800-54958800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chrX:54949000-54955400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chrX:54949000-54955600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chrX:54949000-54957000	Weak transcription	Fetal Heart	heart
24	chrX:54949000-54957400	Weak transcription	Rectal Smooth Muscle	rectum
25	chrX:54949000-54957600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chrX:54949000-54957600	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chrX:54949000-54958400	Strong transcription	H1 Cell Line	embryonic stem cell
28	chrX:54949000-54958600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chrX:54949000-54958800	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chrX:54949200-54955000	Weak transcription	Pancreas	Pancrea
31	chrX:54949200-54956800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chrX:54949200-54957800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chrX:54949200-54958200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chrX:54949200-54958200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chrX:54949200-54960200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chrX:54949400-54954600	Strong transcription	Fetal Lung	lung
37	chrX:54949400-54958200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chrX:54949400-54958600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chrX:54949400-54959000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chrX:54949600-54959400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chrX:54949800-54954800	Weak transcription	Brain Angular Gyrus	brain
42	chrX:54949800-54961000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chrX:54950200-54954600	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chrX:54950200-54955200	Strong transcription	Fetal Muscle Trunk	muscle
45	chrX:54950200-54958400	Strong transcription	Fetal Muscle Leg	muscle
46	chrX:54950200-54958800	Weak transcription	Fetal Intestine Small	intestine
47	chrX:54950400-54958000	Strong transcription	Brain Germinal Matrix	brain
48	chrX:54950600-54955200	Strong transcription	Primary hematopoietic stem cells	blood
49	chrX:54950600-54957400	Strong transcription	Ovary	ovary
50	chrX:54950600-54959000	Strong transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links