Variant report

Variant	rs28840839
Chromosome Location	chr15:52762144-52762145
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	chr15:52758367..52760443-chr15:52760570..52762927,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs13329417	0.87[ASN][1000 genomes]
rs13329510	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1693516	1.00[EUR][1000 genomes]
rs1693517	1.00[EUR][1000 genomes]
rs1693519	1.00[EUR][1000 genomes]
rs1724599	1.00[EUR][1000 genomes]
rs1724600	1.00[EUR][1000 genomes]
rs1724602	1.00[EUR][1000 genomes]
rs2222656	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28401713	0.87[ASN][1000 genomes]
rs28415472	0.87[ASN][1000 genomes]
rs28417081	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28417825	1.00[EUR][1000 genomes]
rs28421476	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28483042	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485251	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28485735	1.00[ASN][1000 genomes]
rs28499517	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28510975	0.87[ASN][1000 genomes]
rs28545705	0.87[ASN][1000 genomes]
rs28556791	1.00[EUR][1000 genomes]
rs28570350	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28578651	0.87[ASN][1000 genomes]
rs28581262	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28613360	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28642806	0.87[ASN][1000 genomes]
rs28663524	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28665952	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28673564	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28682547	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28687913	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28699673	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28729511	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28761013	1.00[ASN][1000 genomes]
rs28786736	1.00[ASN][1000 genomes]
rs28795685	1.00[ASN][1000 genomes]
rs28814017	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28814321	1.00[ASN][1000 genomes]
rs28876722	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168981	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73412972	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73412975	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7342673	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9920195	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52753600-52762600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr15:52757200-52770400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:52757400-52771800	Weak transcription	Primary T cells from cord blood	blood
4	chr15:52758600-52772000	Weak transcription	HUVEC	blood vessel
5	chr15:52758600-52773000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:52758800-52773000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:52759000-52762200	Weak transcription	Psoas Muscle	Psoas
8	chr15:52759000-52772000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr15:52759200-52762200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr15:52759200-52763800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr15:52759200-52770600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:52759200-52771000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr15:52759200-52778200	Weak transcription	Right Atrium	heart
14	chr15:52759400-52762200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:52759400-52763800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr15:52759400-52773000	Weak transcription	Brain Angular Gyrus	brain
17	chr15:52759800-52773000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr15:52760400-52770600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:52761600-52762200	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr15:52761800-52762400	Enhancers	Brain Cingulate Gyrus	brain

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