Variant report

Variant	rs604105
Chromosome Location	chr13:53442344-53442345
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	chr13:53423777..53426647-chr13:53440227..53445526,5	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12100313	0.98[ASN][1000 genomes]
rs1274580	0.98[ASN][1000 genomes]
rs1274581	0.99[ASN][1000 genomes]
rs1274582	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1323117	0.84[ASN][1000 genomes]
rs1323118	0.81[ASN][1000 genomes]
rs1359046	0.86[EUR][1000 genomes]
rs1885848	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1923853	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2764035	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2897999	0.99[ASN][1000 genomes]
rs471680	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886022	0.81[ASN][1000 genomes]
rs489654	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs496890	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs508523	0.99[ASN][1000 genomes]
rs525135	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs537874	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs540528	0.99[ASN][1000 genomes]
rs572545	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs582583	0.91[EUR][1000 genomes]
rs615225	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629671	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636937	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs646902	0.99[ASN][1000 genomes]
rs648146	0.98[ASN][1000 genomes]
rs648232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649523	0.99[ASN][1000 genomes]
rs664608	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs676284	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9316593	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9527030	0.81[ASN][1000 genomes]
rs9536315	0.81[ASN][1000 genomes]
rs9591474	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9596705	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9596709	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9596710	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9788390	0.98[ASN][1000 genomes]
rs9788403	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53441000-53442400	Flanking Active TSS	Dnd41	blood
2	chr13:53441200-53445800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr13:53441400-53442800	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr13:53441600-53442400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr13:53441600-53443000	Enhancers	Brain Germinal Matrix	brain
6	chr13:53441600-53443400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr13:53441600-53444800	Enhancers	GM12878-XiMat	blood
8	chr13:53441600-53445600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:53441800-53442800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr13:53442000-53443000	Enhancers	Fetal Brain Male	brain
11	chr13:53442000-53443200	Enhancers	Fetal Brain Female	brain
12	chr13:53442000-53443600	Enhancers	Fetal Thymus	thymus
13	chr13:53442000-53446600	Enhancers	Fetal Muscle Leg	muscle
14	chr13:53442000-53447000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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