Variant report

Variant	rs62255831
Chromosome Location	chr3:55893668-55893669
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	chr3:55893131..55895315-chr3:55900405..55902843,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12636793	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1379710	0.88[EUR][1000 genomes]
rs1458066	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17056053	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17056061	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17056065	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17056081	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17056090	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17056093	0.81[ASN][1000 genomes]
rs17056098	0.88[ASN][1000 genomes]
rs1902861	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55673265	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55675302	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55682897	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55957219	1.00[ASN][1000 genomes]
rs55967115	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55971093	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57688760	1.00[ASN][1000 genomes]
rs58422259	1.00[ASN][1000 genomes]
rs59611401	1.00[ASN][1000 genomes]
rs62253660	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255821	1.00[ASN][1000 genomes]
rs62255832	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255835	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62256771	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62256772	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62256773	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62256774	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62256778	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6445755	0.88[ASN][1000 genomes]
rs6763408	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6766607	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769408	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790300	1.00[ASN][1000 genomes]
rs73073394	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs733509	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7609626	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617166	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618265	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7631779	1.00[ASN][1000 genomes]
rs7631846	1.00[ASN][1000 genomes]
rs7636943	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638901	1.00[ASN][1000 genomes]
rs7639013	0.82[AMR][1000 genomes]
rs7649504	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs897965	0.82[EUR][1000 genomes]
rs993594	0.83[EUR][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	nsv1013063	chr3:55835413-56173713	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:55889000-55894000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr3:55889200-55894600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:55890400-55893800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:55891800-55895400	Enhancers	Fetal Lung	lung
5	chr3:55891800-55895400	Enhancers	Fetal Stomach	stomach
6	chr3:55891800-55896400	Enhancers	Brain Germinal Matrix	brain
7	chr3:55892400-55894200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:55892400-55895000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:55892600-55894800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:55892600-55895400	Enhancers	Brain Cingulate Gyrus	brain
11	chr3:55892600-55895400	Enhancers	Fetal Kidney	kidney
12	chr3:55892600-55896000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr3:55892800-55894000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:55892800-55894600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr3:55892800-55894600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:55892800-55894600	Enhancers	Brain Hippocampus Middle	brain
17	chr3:55892800-55894800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:55893000-55894000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:55893000-55894000	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr3:55893000-55894200	Enhancers	Brain Anterior Caudate	brain
21	chr3:55893000-55894400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:55893000-55894600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:55893000-55895000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr3:55893000-55908800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:55893200-55895200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:55893200-55895200	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr3:55893400-55894800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr3:55893400-55895800	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr3:55893400-55896000	Weak transcription	Fetal Heart	heart
30	chr3:55893600-55923600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links