Variant report

Variant	rs1746052
Chromosome Location	chr10:44778546-44778547
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:44776762..44778812-chr10:44792922..44795604,2	MCF-7	breast:
2	chr10:44755730..44758552-chr10:44778195..44780852,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237590	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11238977	0.86[CHD][hapmap]
rs1159931	0.87[CHD][hapmap];0.81[JPT][hapmap]
rs1632484	0.86[EUR][1000 genomes]
rs1657344	0.88[EUR][1000 genomes]
rs1657345	0.95[EUR][1000 genomes]
rs1746047	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1746048	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1746049	0.88[EUR][1000 genomes]
rs1746050	0.88[EUR][1000 genomes]
rs2209065	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs2576354	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2576355	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2760670	0.88[ASN][1000 genomes]
rs473501	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs474281	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs479596	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs487465	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs492152	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs494207	0.88[ASN][1000 genomes]
rs498810	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs501120	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs504799	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs510785	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs513391	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs518594	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs522293	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs534079	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs535176	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs535949	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs541483	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs546659	0.88[ASN][1000 genomes]
rs554565	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs559469	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs559580	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs573141	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs579058	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs583489	0.88[ASN][1000 genomes]
rs587375	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs604674	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs605414	0.86[ASN][1000 genomes]
rs605445	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs607363	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs607592	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs607609	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs607760	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs617035	0.87[ASN][1000 genomes]
rs617542	0.88[ASN][1000 genomes]
rs620356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs620828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs622472	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs622956	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs634963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs635612	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs646890	0.88[ASN][1000 genomes]
rs649192	0.88[ASN][1000 genomes]
rs665855	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs670056	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs671765	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs683297	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs684196	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs684521	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs684666	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs687175	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs694425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7082209	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs800330	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs915083	0.91[EUR][1000 genomes];0.93[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1746052	CSGALNACT2	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44774000-44780000	Enhancers	Fetal Brain Male	brain
2	chr10:44775200-44779800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr10:44777000-44779800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr10:44777200-44782800	Weak transcription	Adipose Nuclei	Adipose
5	chr10:44777200-44782800	Weak transcription	Lung	lung
6	chr10:44777400-44780000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr10:44777400-44780000	Weak transcription	Right Ventricle	heart
8	chr10:44777400-44788200	Weak transcription	Right Atrium	heart
9	chr10:44777600-44779800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr10:44777600-44779800	Weak transcription	Left Ventricle	heart
11	chr10:44777600-44780200	Weak transcription	NHDF-Ad	bronchial
12	chr10:44778000-44779000	Enhancers	K562	blood
13	chr10:44778000-44779400	Enhancers	Brain Germinal Matrix	brain
14	chr10:44778200-44779400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr10:44778200-44779400	Enhancers	Fetal Brain Female	brain
16	chr10:44778400-44778600	Enhancers	Fetal Muscle Leg	muscle
17	chr10:44778400-44778600	Enhancers	HSMMtube	muscle
18	chr10:44778400-44778800	Enhancers	Fetal Intestine Large	intestine

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