Variant report

Variant	rs352602
Chromosome Location	chr5:106966332-106966333
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	chr5:106966022..106967957-chr5:106979262..106981193,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1363870	1.00[CHB][hapmap]
rs149382	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs154191	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs164690	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs164691	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs164693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164694	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs164695	0.89[ASN][1000 genomes]
rs164696	0.89[ASN][1000 genomes]
rs164837	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs164970	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26724	0.84[CEU][hapmap];0.83[GIH][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs26726	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs26728	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs26729	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs26730	1.00[CHB][hapmap]
rs26735	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs27550	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs27551	0.87[ASN][1000 genomes]
rs35419	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35534	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs42449	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6887589	0.85[CHB][hapmap];0.86[CHD][hapmap]

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	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs352602	SLC25A46	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106942400-106981600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:106944600-106969200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:106954200-106967600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:106954400-106968800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:106955400-106969000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:106956000-106968200	Weak transcription	A549	lung
7	chr5:106961400-106966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:106962400-106969200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:106962600-106969000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:106963200-106969200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:106963800-106966800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:106964600-106967800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:106964600-106972400	Weak transcription	Fetal Heart	heart
14	chr5:106965200-106966800	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr5:106965600-106969000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr5:106965600-106969400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr5:106965800-106966400	Enhancers	Fetal Lung	lung
18	chr5:106965800-106969000	Weak transcription	Esophagus	oesophagus
19	chr5:106966000-106966800	Enhancers	Stomach Mucosa	stomach
20	chr5:106966200-106967400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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