Variant report

Variant	rs12553507
Chromosome Location	chr9:104077757-104077758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:104076229..104078095-chr9:104085107..104087859,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10125731	0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10512279	0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10989462	0.85[JPT][hapmap]
rs10989469	0.84[ASN][1000 genomes]
rs10989471	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs11790209	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11790501	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11792655	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12341244	0.80[JPT][hapmap]
rs12341316	0.85[JPT][hapmap]
rs12553209	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12683393	1.00[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12683674	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12684829	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13289023	0.85[JPT][hapmap]
rs13296052	0.85[JPT][hapmap]
rs1341769	0.87[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1891219	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1935240	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2275683	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs34553293	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35846126	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3780531	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]
rs3944892	0.85[JPT][hapmap]
rs4480176	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6479049	0.88[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	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7861116	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7868832	0.81[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7869625	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12553507	ALG2	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104073000-104088600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr9:104073800-104082600	Weak transcription	Brain Anterior Caudate	brain
3	chr9:104074200-104080800	Enhancers	Liver	Liver
4	chr9:104074400-104081200	Weak transcription	Brain Substantia Nigra	brain
5	chr9:104075400-104079600	Weak transcription	Fetal Brain Female	brain
6	chr9:104075600-104079400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr9:104075600-104079800	Weak transcription	Fetal Brain Male	brain
8	chr9:104075600-104081800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:104075600-104088600	Weak transcription	Brain Germinal Matrix	brain
10	chr9:104075800-104079600	Weak transcription	Brain Hippocampus Middle	brain
11	chr9:104077200-104079000	Enhancers	A549	lung
12	chr9:104077600-104078000	Enhancers	HSMMtube	muscle
13	chr9:104077600-104078200	Enhancers	Fetal Muscle Leg	muscle
14	chr9:104077600-104078400	Enhancers	Fetal Lung	lung
15	chr9:104077600-104078400	Flanking Active TSS	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links