Variant report

Variant	rs1562490
Chromosome Location	chr3:134405574-134405575
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11915953	0.95[EUR][1000 genomes]
rs12630872	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13071939	1.00[EUR][1000 genomes]
rs1447687	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466078	1.00[EUR][1000 genomes]
rs1466083	1.00[EUR][1000 genomes]
rs1562484	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1562486	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28514359	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4245901	1.00[EUR][1000 genomes]
rs4455359	1.00[TSI][hapmap]
rs4955445	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4955473	0.95[EUR][1000 genomes]
rs4955475	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57308880	0.95[EUR][1000 genomes]
rs59457762	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59501108	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60499703	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61179905	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61695122	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6439513	0.86[EUR][1000 genomes]
rs6439515	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6769991	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6770549	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6784382	0.82[EUR][1000 genomes]
rs6807467	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72978221	1.00[EUR][1000 genomes]
rs72978223	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72978225	1.00[EUR][1000 genomes]
rs72978227	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72978266	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72978269	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72978274	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72978284	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72978288	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72978290	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7610168	1.00[TSI][hapmap]
rs7620383	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1562490	SIRPG	trans	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134400400-134412600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:134402000-134411600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:134403400-134407800	Enhancers	Fetal Muscle Leg	muscle
4	chr3:134404000-134406400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:134404400-134406200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:134404400-134407600	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr3:134404600-134405800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:134404600-134406200	Enhancers	Osteobl	bone
9	chr3:134404600-134407000	Enhancers	Psoas Muscle	Psoas
10	chr3:134404800-134405800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:134404800-134405800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr3:134404800-134405800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr3:134404800-134405800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr3:134404800-134405800	Enhancers	HSMM	muscle
15	chr3:134404800-134406000	Enhancers	NH-A	brain
16	chr3:134404800-134406000	Enhancers	NHDF-Ad	bronchial
17	chr3:134404800-134406200	Enhancers	HSMMtube	muscle
18	chr3:134405000-134405800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:134405000-134405800	Enhancers	NHLF	lung
20	chr3:134405000-134409200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:134405200-134405800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links