Variant report

Variant	rs17056053
Chromosome Location	chr3:55894537-55894538
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: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12636793	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1379710	0.85[EUR][1000 genomes]
rs1458066	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17056061	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17056065	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17056081	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17056090	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17056093	0.83[AFR][1000 genomes]
rs17056098	0.82[ASN][1000 genomes]
rs1902861	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55673265	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55675302	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55682897	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55957219	0.94[ASN][1000 genomes]
rs55967115	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs55971093	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57688760	0.94[ASN][1000 genomes]
rs58422259	0.94[ASN][1000 genomes]
rs59611401	0.94[ASN][1000 genomes]
rs62253660	0.82[ASN][1000 genomes]
rs62255821	0.94[ASN][1000 genomes]
rs62255831	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62255832	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62255835	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62256771	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62256772	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62256773	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62256774	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62256778	0.82[ASN][1000 genomes]
rs6445755	0.82[ASN][1000 genomes]
rs6763408	0.82[ASN][1000 genomes]
rs6766607	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6769408	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6790300	0.94[ASN][1000 genomes]
rs73073394	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs733509	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7609626	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7617166	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7618265	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7631779	0.94[ASN][1000 genomes]
rs7631846	0.94[ASN][1000 genomes]
rs7636943	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7638901	0.94[ASN][1000 genomes]
rs7639013	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7649504	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9815155	1.00[CHB][hapmap];1.00[JPT][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	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:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:55889200-55894600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:55891800-55895400	Enhancers	Fetal Lung	lung
3	chr3:55891800-55895400	Enhancers	Fetal Stomach	stomach
4	chr3:55891800-55896400	Enhancers	Brain Germinal Matrix	brain
5	chr3:55892400-55895000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:55892600-55894800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:55892600-55895400	Enhancers	Brain Cingulate Gyrus	brain
8	chr3:55892600-55895400	Enhancers	Fetal Kidney	kidney
9	chr3:55892600-55896000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr3:55892800-55894600	Enhancers	H1 Cell Line	embryonic stem cell
11	chr3:55892800-55894600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:55892800-55894600	Enhancers	Brain Hippocampus Middle	brain
13	chr3:55892800-55894800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:55893000-55894600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:55893000-55895000	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:55893000-55908800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:55893200-55895200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:55893200-55895200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr3:55893400-55894800	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr3:55893400-55895800	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr3:55893400-55896000	Weak transcription	Fetal Heart	heart
22	chr3:55893600-55923600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:55893800-55895000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:55894000-55894800	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr3:55894000-55895000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:55894000-55901400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:55894200-55894800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr3:55894200-55895400	Enhancers	Fetal Brain Male	brain
29	chr3:55894200-55895800	Enhancers	Brain Substantia Nigra	brain
30	chr3:55894400-55894800	Enhancers	Fetal Brain Female	brain
31	chr3:55894400-55894800	Enhancers	Fetal Intestine Small	intestine

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