Variant report

Variant	rs1746048
Chromosome Location	chr10:44775824-44775825
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11238973	0.89[ASN][1000 genomes]
rs11238974	0.89[ASN][1000 genomes]
rs11238975	0.89[ASN][1000 genomes]
rs11238977	0.81[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs1159931	0.80[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs12414524	0.84[ASN][1000 genomes]
rs1469894	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs1632484	0.93[EUR][1000 genomes]
rs1657344	0.83[EUR][1000 genomes]
rs1657345	0.89[EUR][1000 genomes]
rs17155848	0.84[ASN][1000 genomes]
rs17155973	0.89[ASN][1000 genomes]
rs17155977	0.89[ASN][1000 genomes]
rs1746047	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1746049	0.95[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1746050	0.95[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1746052	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1998501	0.89[ASN][1000 genomes]
rs2209065	0.80[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs2576354	0.90[EUR][1000 genomes]
rs2576355	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2862118	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs473501	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs474281	0.94[EUR][1000 genomes]
rs475926	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs479596	1.00[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs487465	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs492152	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4948867	0.84[ASN][1000 genomes]
rs498810	0.93[EUR][1000 genomes]
rs501120	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs504799	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs510785	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs513391	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs518594	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs522293	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs534079	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs535176	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs535949	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs541483	0.92[EUR][1000 genomes]
rs554565	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs559469	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs559580	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs573141	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs579058	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs583489	0.80[AMR][1000 genomes]
rs587375	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs604674	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs605445	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs607363	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs607592	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs607609	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs607760	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs620356	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs620828	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs622472	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs622956	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs634963	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs635612	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs665855	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs670056	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs671765	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs683297	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs684196	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs684521	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs684666	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs687175	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs694425	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7082209	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs746298	0.84[ASN][1000 genomes]
rs800330	0.81[JPT][hapmap]
rs915083	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038511	chr10:44596885-44870030	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv508579	chr10:44709770-44799256	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Coronary heart disease	21378990	GWAS catalog
Myocardial infarction (early onset)	19198609	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1746048	CSGALNACT2	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44774000-44776400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr10:44774000-44777000	Enhancers	NHLF	lung
3	chr10:44774000-44780000	Enhancers	Fetal Brain Male	brain
4	chr10:44774200-44776000	Enhancers	HSMMtube	muscle
5	chr10:44774200-44777400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr10:44774600-44776600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr10:44774600-44776800	Enhancers	Colon Smooth Muscle	Colon
8	chr10:44774600-44777000	Enhancers	Fetal Brain Female	brain
9	chr10:44775000-44777000	Enhancers	Brain Germinal Matrix	brain
10	chr10:44775200-44779800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr10:44775600-44777000	Enhancers	Aorta	Aorta
12	chr10:44775800-44776400	Enhancers	Adipose Nuclei	Adipose
13	chr10:44775800-44776600	Flanking Active TSS	NHDF-Ad	bronchial
14	chr10:44775800-44777600	Enhancers	Fetal Muscle Leg	muscle

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