Variant report

Variant	rs12851962
Chromosome Location	chrX:54950747-54950748
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chrX:54950731-54950889	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
TRO	TF binding region
ENSG00000221750	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1043031	0.94[CEU][hapmap];0.80[JPT][hapmap];0.97[TSI][hapmap]
rs1043034	0.94[CEU][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap]
rs1043044	0.94[CEU][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap]
rs11555927	0.86[MKK][hapmap]
rs12014660	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap]
rs12858090	0.94[CEU][hapmap];0.81[JPT][hapmap]
rs12858147	0.94[CEU][hapmap];0.80[JPT][hapmap]
rs2005463	1.00[ASW][hapmap];0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs2071932	0.94[CEU][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap]
rs2071933	0.94[CEU][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap]
rs2071934	0.94[CEU][hapmap];0.81[JPT][hapmap]
rs2273138	1.00[CEU][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap]
rs2281383	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2361189	0.94[CEU][hapmap]
rs3765479	1.00[CEU][hapmap];0.96[GIH][hapmap];0.97[TSI][hapmap]
rs4826364	0.89[CEU][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.94[TSI][hapmap]
rs4826365	0.89[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs5914241	1.00[CEU][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap]
rs5960055	1.00[CEU][hapmap];0.96[GIH][hapmap];0.97[TSI][hapmap]
rs5960060	1.00[MKK][hapmap]
rs5960336	0.94[CEU][hapmap];0.81[JPT][hapmap]
rs5960385	1.00[MKK][hapmap]
rs6611391	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs743974	0.94[CEU][hapmap];0.91[TSI][hapmap]
rs763183	0.94[CEU][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap]
rs763184	0.94[CEU][hapmap];0.81[JPT][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12851962	TRO	cis	lymphoblastoid	seeQTL
rs12851962	TRO	cis	multi-tissue	Pritchard

Chromatin state (count:79 , 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:54948600-54950800	Weak transcription	Fetal Intestine Large	intestine
7	chrX:54948600-54956400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chrX:54948600-54956800	Weak transcription	HSMM	muscle
9	chrX:54948600-54957800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chrX:54948600-54957800	Weak transcription	HepG2	liver
11	chrX:54948600-54959000	Weak transcription	Primary T cells from cord blood	blood
12	chrX:54948800-54950800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chrX:54948800-54950800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chrX:54948800-54950800	Weak transcription	Psoas Muscle	Psoas
15	chrX:54948800-54951000	Weak transcription	Fetal Thymus	thymus
16	chrX:54948800-54951200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chrX:54948800-54951200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chrX:54948800-54951200	Weak transcription	Fetal Brain Male	brain
19	chrX:54948800-54953000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chrX:54948800-54953400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chrX:54948800-54954200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chrX:54948800-54955000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chrX:54948800-54955000	Weak transcription	Thymus	Thymus
24	chrX:54948800-54955200	Weak transcription	Brain Cingulate Gyrus	brain
25	chrX:54948800-54957000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chrX:54948800-54957400	Weak transcription	Right Atrium	heart
27	chrX:54948800-54957800	Weak transcription	Right Ventricle	heart
28	chrX:54948800-54957800	Weak transcription	Osteobl	bone
29	chrX:54948800-54958200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chrX:54948800-54958600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
31	chrX:54948800-54958800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chrX:54949000-54951000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
33	chrX:54949000-54951000	Weak transcription	Brain Hippocampus Middle	brain
34	chrX:54949000-54951200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chrX:54949000-54952600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chrX:54949000-54953000	Weak transcription	Brain Anterior Caudate	brain
37	chrX:54949000-54953600	Weak transcription	Primary B cells from peripheral blood	blood
38	chrX:54949000-54954400	Weak transcription	Brain Substantia Nigra	brain
39	chrX:54949000-54955400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chrX:54949000-54955600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chrX:54949000-54957000	Weak transcription	Fetal Heart	heart
42	chrX:54949000-54957400	Weak transcription	Rectal Smooth Muscle	rectum
43	chrX:54949000-54957600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chrX:54949000-54957600	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chrX:54949000-54958400	Strong transcription	H1 Cell Line	embryonic stem cell
46	chrX:54949000-54958600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chrX:54949000-54958800	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chrX:54949200-54951000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chrX:54949200-54953600	Strong transcription	Fetal Stomach	stomach
50	chrX:54949200-54955000	Weak transcription	Pancreas	Pancrea

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