Variant report

Variant	rs13419598
Chromosome Location	chr2:72923070-72923071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10084347	1.00[MEX][hapmap]
rs10170993	1.00[AMR][1000 genomes]
rs10173937	1.00[MKK][hapmap]
rs10179254	1.00[MEX][hapmap]
rs10190863	1.00[AMR][1000 genomes]
rs10203912	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10206245	1.00[MEX][hapmap]
rs13385811	1.00[MEX][hapmap]
rs13391821	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs13397743	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs13413528	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13414291	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13426691	1.00[MEX][hapmap]
rs13429668	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs13431249	1.00[MEX][hapmap]
rs28793596	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4852886	1.00[YRI][hapmap]

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	nsv874265	chr2:72789764-72982609	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13419598	PRRX1	trans	lymphoblastoid	seeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72896800-72943000	Weak transcription	Primary T cells from cord blood	blood
2	chr2:72903600-72937400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:72904400-72939000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:72905600-72943200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:72905800-72984400	Weak transcription	Aorta	Aorta
6	chr2:72912200-72942800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:72913400-72945000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:72917000-72950000	Weak transcription	Brain Angular Gyrus	brain
9	chr2:72917200-72946200	Weak transcription	HMEC	breast
10	chr2:72917400-72944800	Weak transcription	NHEK	skin
11	chr2:72919800-72924000	Enhancers	Fetal Heart	heart
12	chr2:72920000-72923600	Enhancers	Brain Cingulate Gyrus	brain
13	chr2:72920400-72945000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:72921200-72924000	Enhancers	Ovary	ovary
15	chr2:72922000-72946200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:72922200-72923400	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:72922200-72942800	Weak transcription	Placenta	Placenta
18	chr2:72922400-72923200	Enhancers	Colon Smooth Muscle	Colon
19	chr2:72922400-72923400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:72922400-72923400	Weak transcription	Small Intestine	intestine
21	chr2:72922400-72925200	Weak transcription	Brain Anterior Caudate	brain
22	chr2:72922400-72929800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:72922400-72939400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:72922400-72941000	Weak transcription	Left Ventricle	heart
25	chr2:72922400-72942800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:72922400-72945800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:72922400-72949800	Weak transcription	Fetal Brain Female	brain
28	chr2:72922400-72972000	Weak transcription	Right Ventricle	heart
29	chr2:72922400-72976200	Weak transcription	Psoas Muscle	Psoas
30	chr2:72922600-72923200	Enhancers	A549	lung
31	chr2:72922600-72923600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:72922600-72924000	Enhancers	K562	blood
33	chr2:72922600-72925600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:72922600-72929200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:72922600-72933400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:72922600-72942800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:72922600-72951000	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:72922800-72927000	Weak transcription	Fetal Brain Male	brain
39	chr2:72922800-72927600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:72922800-72939400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:72922800-72949600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:72923000-72923200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr2:72923000-72932600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:72923000-72939400	Weak transcription	HepG2	liver
45	chr2:72923000-72944600	Weak transcription	Fetal Lung	lung
46	chr2:72923000-72945600	Weak transcription	Fetal Stomach	stomach
47	chr2:72923000-72972800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:72923000-73008600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links