Variant report

Variant	rs2293275
Chromosome Location	chr2:48921375-48921376
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	chr1:110595729..110598402-chr2:48919078..48921573,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10198501	0.85[ASW][hapmap];0.84[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.92[YRI][hapmap]
rs10208754	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.83[AMR][1000 genomes]
rs10495955	0.90[CHD][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.80[AMR][1000 genomes]
rs11125178	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11125179	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11685904	0.90[CHD][hapmap]
rs11691408	1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.88[ASN][1000 genomes]
rs11892581	1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11899239	0.81[AMR][1000 genomes]
rs11901588	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs12473064	0.82[AMR][1000 genomes]
rs12713012	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs12997569	0.90[CHD][hapmap]
rs13022553	1.00[CHB][hapmap]
rs13022734	0.83[AMR][1000 genomes]
rs13024367	1.00[CHB][hapmap]
rs1404051	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1464727	0.81[CEU][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1464729	1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap]
rs1524148	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1524155	0.82[CEU][hapmap];0.89[AMR][1000 genomes]
rs1589749	0.90[CHD][hapmap]
rs17326209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17326251	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1916838	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs1996968	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1996969	1.00[CHD][hapmap]
rs2056581	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2103113	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2349099	0.90[CHD][hapmap]
rs2349101	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28666758	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34378457	0.88[ASN][1000 genomes]
rs34757099	0.97[ASN][1000 genomes]
rs34790224	0.93[ASN][1000 genomes]
rs3792241	0.81[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap]
rs3792243	0.90[CHD][hapmap]
rs3792246	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3811516	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62137532	0.93[ASN][1000 genomes]
rs6545051	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6545054	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6710333	0.80[AMR][1000 genomes]
rs6730379	1.00[CHB][hapmap]
rs6738387	0.90[CHD][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes]
rs6739692	0.82[AMR][1000 genomes]
rs6741840	1.00[CHB][hapmap]
rs6746530	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6746623	1.00[CHB][hapmap]
rs6747475	1.00[CHB][hapmap]
rs7583310	0.83[ASN][1000 genomes]
rs7587112	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv833992	chr2:48814223-48998037	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2293275	STON1-GTF2A1L	cis	parietal	SCAN
rs2293275	STON1-GTF2A1L	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48918000-48926400	Weak transcription	Adipose Nuclei	Adipose
2	chr2:48919000-48922800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr2:48919000-48923400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:48919200-48921400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr2:48919200-48923400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr2:48919400-48921400	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr2:48919400-48923000	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr2:48919600-48922400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:48919600-48922600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:48919800-48926600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:48920000-48921400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:48920000-48921800	Enhancers	Stomach Smooth Muscle	stomach
13	chr2:48920200-48921600	Enhancers	Ovary	ovary
14	chr2:48920200-48926600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:48920400-48926600	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:48920600-48921800	Enhancers	Placenta Amnion	Placenta Amnion
17	chr2:48920600-48922000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:48920600-48922000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:48920600-48922000	Enhancers	NHLF	lung
20	chr2:48920800-48921400	Enhancers	HMEC	breast
21	chr2:48920800-48921600	Enhancers	Fetal Kidney	kidney
22	chr2:48920800-48921600	Enhancers	NHEK	skin
23	chr2:48920800-48921600	Enhancers	Osteobl	bone
24	chr2:48920800-48922000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:48920800-48922200	Enhancers	H1 Cell Line	embryonic stem cell
26	chr2:48921000-48921800	Active TSS	NH-A	brain
27	chr2:48921000-48922000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:48921200-48921400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr2:48921200-48921600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr2:48921200-48922200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:48921200-48922200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr2:48921200-48922800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:48921200-48923200	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links