Variant report

Variant	rs3780531
Chromosome Location	chr9:104074872-104074873
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	chr9:104069628..104072510-chr9:104073819..104075636,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10125731	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10512279	0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10989462	0.85[JPT][hapmap]
rs10989469	0.84[ASN][1000 genomes]
rs10989471	0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs11790209	0.94[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11790501	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11792655	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12341244	0.80[JPT][hapmap]
rs12341316	0.85[JPT][hapmap]
rs12553209	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12553507	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12683393	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.95[ASN][1000 genomes]
rs12683674	0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12684829	0.85[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13289023	0.85[JPT][hapmap]
rs13296052	0.85[JPT][hapmap]
rs1341769	0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1891219	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1935240	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2275683	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs34553293	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35846126	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3944892	0.85[JPT][hapmap]
rs4480176	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6479049	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7023477	0.85[JPT][hapmap]
rs7023799	0.95[ASN][1000 genomes]
rs7034058	0.85[JPT][hapmap]
rs7035407	0.84[JPT][hapmap]
rs7040055	0.94[ASN][1000 genomes]
rs7848242	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7861116	0.97[ASN][1000 genomes]
rs7868832	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869625	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv1037157	chr9:104045761-104149233	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1049740	chr9:104049624-104075825	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3780531	ALG2	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104069400-104075000	Weak transcription	Fetal Brain Male	brain
2	chr9:104069800-104075000	Weak transcription	Brain Germinal Matrix	brain
3	chr9:104069800-104075000	Weak transcription	Fetal Muscle Leg	muscle
4	chr9:104070800-104075000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr9:104072400-104075800	Enhancers	Brain Hippocampus Middle	brain
6	chr9:104073000-104088600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:104073600-104075200	Enhancers	Brain Angular Gyrus	brain
8	chr9:104073800-104075200	Enhancers	HSMM	muscle
9	chr9:104073800-104082600	Weak transcription	Brain Anterior Caudate	brain
10	chr9:104074200-104075200	Enhancers	HepG2	liver
11	chr9:104074200-104075400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:104074200-104075400	Enhancers	Fetal Lung	lung
13	chr9:104074200-104075400	Enhancers	HSMMtube	muscle
14	chr9:104074200-104080800	Enhancers	Liver	Liver
15	chr9:104074400-104075000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr9:104074400-104081200	Weak transcription	Brain Substantia Nigra	brain
17	chr9:104074600-104075200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr9:104074600-104077200	Weak transcription	A549	lung
19	chr9:104074800-104075400	Enhancers	Adipose Nuclei	Adipose
20	chr9:104074800-104075800	Enhancers	Cortex derived primary cultured neurospheres	brain

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