Variant report

Variant	rs848827
Chromosome Location	chr5:106859484-106859485
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:106794093..106796803-chr5:106857848..106860551,2	MCF-7	breast:
2	chr5:106848396..106850133-chr5:106859068..106861011,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs152554	0.96[EUR][1000 genomes]
rs153189	0.90[ASN][1000 genomes]
rs163895	1.00[CHB][hapmap]
rs1966892	1.00[CHB][hapmap]
rs250251	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs250253	0.96[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs352605	1.00[CHB][hapmap]
rs388016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs395561	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs446774	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6879279	1.00[CHB][hapmap]
rs7443170	1.00[CHB][hapmap]
rs848828	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[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
rs848827	SLC25A46	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106842400-106880000	Weak transcription	Gastric	stomach
2	chr5:106848800-106865000	Weak transcription	Right Atrium	heart
3	chr5:106852800-106860200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr5:106856000-106859800	Weak transcription	Stomach Mucosa	stomach
5	chr5:106856000-106865000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:106856000-106868600	Weak transcription	Right Ventricle	heart
7	chr5:106856400-106865000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:106856600-106865000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:106856600-106865000	Weak transcription	Aorta	Aorta
10	chr5:106856800-106862000	Weak transcription	Fetal Heart	heart
11	chr5:106857400-106859600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:106857400-106868000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:106857600-106860600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:106857600-106861000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:106857800-106867200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:106858400-106860200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr5:106858400-106860400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr5:106858600-106860600	Enhancers	Fetal Kidney	kidney
19	chr5:106858600-106860800	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr5:106858800-106860200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr5:106858800-106860600	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr5:106858800-106860600	Enhancers	Placenta Amnion	Placenta Amnion
23	chr5:106859000-106859600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr5:106859000-106859600	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr5:106859000-106859600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:106859000-106860000	Enhancers	H9 Cell Line	embryonic stem cell
27	chr5:106859000-106860000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr5:106859000-106860200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:106859000-106860200	Enhancers	Left Ventricle	heart
30	chr5:106859000-106860400	Flanking Active TSS	A549	lung
31	chr5:106859000-106860400	Enhancers	HSMM	muscle
32	chr5:106859000-106860600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:106859000-106860600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr5:106859000-106860600	Enhancers	NHEK	skin
35	chr5:106859000-106860800	Enhancers	HMEC	breast
36	chr5:106859000-106861000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:106859200-106859800	Weak transcription	HSMMtube	muscle
38	chr5:106859200-106860000	Enhancers	H1 Cell Line	embryonic stem cell
39	chr5:106859200-106860200	Enhancers	Esophagus	oesophagus
40	chr5:106859200-106862000	Weak transcription	Pancreas	Pancrea
41	chr5:106859400-106860000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:106859400-106861400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr5:106859400-106861800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr5:106859400-106862200	Weak transcription	Fetal Lung	lung
45	chr5:106859400-106865000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links