Variant report

Variant	rs579839
Chromosome Location	chr13:52437157-52437158
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	chr13:52376935..52378764-chr13:52436044..52437882,2	MCF-7	breast:
2	chr13:52433416..52435036-chr13:52436676..52439385,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231856	Chromatin interaction
ENSG00000102796	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12874582	1.00[ASN][1000 genomes]
rs1535577	1.00[CEU][hapmap]
rs17076052	1.00[ASN][1000 genomes]
rs1924614	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924615	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924618	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408530	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28429889	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485335	1.00[ASN][1000 genomes]
rs34507703	1.00[ASN][1000 genomes]
rs34595679	1.00[ASN][1000 genomes]
rs35382547	1.00[ASN][1000 genomes]
rs35824984	1.00[ASN][1000 genomes]
rs4605048	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs481797	1.00[CEU][hapmap]
rs549831	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575555	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577331	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578134	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58050745	1.00[ASN][1000 genomes]
rs58919798	1.00[ASN][1000 genomes]
rs61957362	1.00[ASN][1000 genomes]
rs61957363	1.00[ASN][1000 genomes]
rs61957365	1.00[ASN][1000 genomes]
rs61957367	1.00[ASN][1000 genomes]
rs61957391	1.00[ASN][1000 genomes]
rs61957414	1.00[ASN][1000 genomes]
rs7323551	1.00[ASN][1000 genomes]
rs7324468	1.00[CEU][hapmap]
rs7333241	0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7336182	1.00[ASN][1000 genomes]
rs7338168	1.00[ASN][1000 genomes]
rs932912	1.00[ASN][1000 genomes]
rs9596597	1.00[CEU][hapmap]
rs9596601	1.00[CEU][hapmap]

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	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52433800-52479400	Weak transcription	HepG2	liver
2	chr13:52435400-52437200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr13:52435400-52437400	Enhancers	HUVEC	blood vessel
4	chr13:52436000-52437400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr13:52436000-52438000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr13:52436600-52438000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr13:52436600-52438200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr13:52436600-52438200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr13:52437000-52437600	Enhancers	Primary hematopoietic stem cells	blood
10	chr13:52437000-52437600	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr13:52437000-52437600	Enhancers	Dnd41	blood
12	chr13:52437000-52438000	Enhancers	Fetal Thymus	thymus

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