Variant report

Variant	rs352603
Chromosome Location	chr5:106894003-106894004
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:106892732..106894780-chr5:106905929..106907820,4	MCF-7	breast:
2	chr5:106893133..106894878-chr5:107007816..107009967,2	MCF-7	breast:
3	chr5:106878075..106880996-chr5:106890627..106894007,3	MCF-7	breast:
4	chr5:106891290..106894903-chr5:107005448..107008680,4	MCF-7	breast:
5	chr5:106892845..106895575-chr5:106898409..106900796,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184349	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs341273	0.84[YRI][hapmap];0.85[EUR][1000 genomes]
rs341275	0.84[YRI][hapmap];0.85[EUR][1000 genomes]
rs342602	0.85[EUR][1000 genomes]
rs342605	0.84[YRI][hapmap];0.85[EUR][1000 genomes]
rs342606	0.84[EUR][1000 genomes]
rs352604	0.94[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs352606	0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs352607	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs352610	0.82[ASW][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs457369	0.93[CEU][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs849520	0.91[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	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
rs352603	SLC25A46	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106879000-106899200	Weak transcription	Fetal Stomach	stomach
2	chr5:106881600-106899600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:106884600-106896400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:106885600-106894800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:106885600-106896400	Weak transcription	Right Atrium	heart
6	chr5:106887200-106899400	Weak transcription	Fetal Lung	lung
7	chr5:106887200-106906800	Weak transcription	Right Ventricle	heart
8	chr5:106889400-106903000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:106890000-106895000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr5:106890000-106895000	Enhancers	NHEK	skin
11	chr5:106890000-106898000	Enhancers	Fetal Heart	heart
12	chr5:106890200-106900800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:106890400-106894800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:106890400-106895000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:106891000-106899800	Weak transcription	Aorta	Aorta
16	chr5:106891400-106895000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:106891400-106895000	Enhancers	HMEC	breast
18	chr5:106892000-106901800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:106892200-106895600	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr5:106892600-106894400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr5:106892600-106895000	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr5:106892600-106895400	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr5:106892600-106895400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr5:106892800-106894800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:106892800-106895600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:106892800-106895600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:106892800-106895800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr5:106892800-106895800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr5:106892800-106899800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr5:106893000-106895200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:106893000-106896400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr5:106893200-106894600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr5:106893200-106894800	Weak transcription	Placenta	Placenta
34	chr5:106893200-106894800	Weak transcription	Left Ventricle	heart
35	chr5:106893200-106901800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr5:106893400-106894400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:106893400-106895400	Weak transcription	NHLF	lung
38	chr5:106893400-106901600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:106893600-106898200	Enhancers	A549	lung
40	chr5:106893800-106894200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr5:106893800-106894800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:106893800-106906000	Weak transcription	NHDF-Ad	bronchial
43	chr5:106894000-106894800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr5:106894000-106902000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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