Variant report

Variant	rs649523
Chromosome Location	chr13:53440459-53440460
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:53423777..53426647-chr13:53440227..53445526,5	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11617253	0.88[EUR][1000 genomes]
rs12100313	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12100317	0.89[EUR][1000 genomes]
rs1274580	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1274581	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1274582	0.98[ASN][1000 genomes]
rs1323117	0.84[ASN][1000 genomes]
rs1323118	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1885848	0.98[ASN][1000 genomes]
rs1923853	0.84[ASN][1000 genomes]
rs2236363	0.87[EUR][1000 genomes]
rs2764035	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2897999	0.98[ASN][1000 genomes]
rs3742300	0.87[EUR][1000 genomes]
rs3742301	0.87[EUR][1000 genomes]
rs4143183	0.89[EUR][1000 genomes]
rs471680	0.99[ASN][1000 genomes]
rs4886022	0.81[ASN][1000 genomes]
rs489654	0.99[ASN][1000 genomes]
rs496890	0.94[ASN][1000 genomes]
rs508523	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525135	0.98[ASN][1000 genomes]
rs537874	0.98[ASN][1000 genomes]
rs540528	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572545	0.96[ASN][1000 genomes]
rs604105	0.99[ASN][1000 genomes]
rs615225	0.99[ASN][1000 genomes]
rs61950421	0.88[EUR][1000 genomes]
rs629671	0.99[ASN][1000 genomes]
rs636937	0.98[ASN][1000 genomes]
rs646902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs648146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs648232	0.99[ASN][1000 genomes]
rs664608	0.94[ASN][1000 genomes]
rs676284	0.98[ASN][1000 genomes]
rs67683610	0.88[EUR][1000 genomes]
rs9316593	0.82[ASN][1000 genomes]
rs9527030	0.81[ASN][1000 genomes]
rs9536315	0.81[ASN][1000 genomes]
rs9591474	0.84[ASN][1000 genomes]
rs9596705	0.98[ASN][1000 genomes]
rs9596709	0.85[ASN][1000 genomes]
rs9596710	0.85[ASN][1000 genomes]
rs9788389	0.89[EUR][1000 genomes]
rs9788390	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9788403	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv1810064	chr13:53412849-53441018	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv1822518	chr13:53412849-53441018	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1829072	chr13:53412849-53441018	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv455889	chr13:53419139-53466127	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv561661	chr13:53419139-53466127	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv900090	chr13:53429453-53495715	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs649523	EBPL	cis	parietal	SCAN
rs649523	RB1	cis	parietal	SCAN
rs649523	LOC220429	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53430800-53441400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr13:53436200-53441600	Weak transcription	GM12878-XiMat	blood
3	chr13:53437200-53441200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr13:53437200-53441400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr13:53437400-53441600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:53438600-53441000	Enhancers	Dnd41	blood
7	chr13:53439200-53441200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr13:53439400-53441600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:53439600-53441600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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