Variant report

Variant	rs28642806
Chromosome Location	chr15:52806439-52806440
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52805292..52807853-chr15:52807856..52810377,2	MCF-7	breast:
2	chr15:52805507..52810026-chr15:52819319..52821633,5	MCF-7	breast:
3	chr15:52806204..52808038-chr15:52817695..52819356,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197535	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs13329417	1.00[AMR][1000 genomes]
rs13329510	0.87[ASN][1000 genomes]
rs2222656	0.87[ASN][1000 genomes]
rs28366864	1.00[AMR][1000 genomes]
rs28401713	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28415069	1.00[AMR][1000 genomes]
rs28417081	1.00[ASN][1000 genomes]
rs28483042	0.87[ASN][1000 genomes]
rs28485735	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28488423	1.00[AMR][1000 genomes]
rs28510975	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28515624	1.00[AMR][1000 genomes]
rs28534436	1.00[AMR][1000 genomes]
rs28545705	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28570350	0.87[ASN][1000 genomes]
rs28578651	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581262	1.00[ASN][1000 genomes]
rs28589619	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28649737	1.00[AMR][1000 genomes]
rs28656089	0.81[AFR][1000 genomes]
rs28665952	1.00[ASN][1000 genomes]
rs28673564	0.94[ASN][1000 genomes]
rs28687913	0.87[ASN][1000 genomes]
rs28699673	1.00[ASN][1000 genomes]
rs28701803	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28711556	1.00[AFR][1000 genomes]
rs28761013	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28786736	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28787300	0.92[AFR][1000 genomes]
rs28795685	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28814017	1.00[ASN][1000 genomes]
rs28814321	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28840839	0.87[ASN][1000 genomes]
rs28863588	0.81[AFR][1000 genomes]
rs28876722	0.87[ASN][1000 genomes]
rs3764226	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7168981	1.00[ASN][1000 genomes]
rs73412972	1.00[ASN][1000 genomes]
rs73412975	1.00[ASN][1000 genomes]
rs73414913	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7342673	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52778600-52812400	Weak transcription	Right Ventricle	heart
2	chr15:52786400-52812400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:52789600-52806600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr15:52792000-52815200	Weak transcription	NHLF	lung
5	chr15:52796800-52811200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:52796800-52819400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr15:52796800-52820000	Weak transcription	Primary T cells from cord blood	blood
8	chr15:52797000-52815200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:52797400-52810200	Weak transcription	Primary B cells from cord blood	blood
10	chr15:52797600-52819800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr15:52800800-52808600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:52801000-52808400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr15:52801800-52810600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:52802000-52809600	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr15:52802400-52808400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr15:52802400-52810800	Weak transcription	HSMMtube	muscle
17	chr15:52802800-52809400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:52803000-52806600	Weak transcription	Psoas Muscle	Psoas
19	chr15:52803000-52807200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr15:52803400-52806600	Weak transcription	Right Atrium	heart
21	chr15:52803400-52812400	Weak transcription	Left Ventricle	heart
22	chr15:52803400-52812400	Weak transcription	Spleen	Spleen
23	chr15:52803800-52806600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr15:52803800-52812200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr15:52803800-52812600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:52803800-52814800	Weak transcription	NHDF-Ad	bronchial
27	chr15:52804000-52806600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:52804000-52806600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:52804000-52806600	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:52804000-52808800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:52804000-52809200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:52804000-52810600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:52804000-52812400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr15:52804000-52812600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr15:52804000-52814000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:52804600-52808400	Weak transcription	Brain Angular Gyrus	brain
37	chr15:52805200-52812400	Weak transcription	Brain Anterior Caudate	brain
38	chr15:52805400-52807800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:52805400-52810000	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr15:52805400-52810200	Weak transcription	Adipose Nuclei	Adipose
41	chr15:52805600-52807600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:52805800-52807400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:52805800-52807400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:52805800-52807400	Enhancers	NHEK	skin
45	chr15:52805800-52807600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr15:52805800-52809800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:52806000-52807400	Enhancers	HMEC	breast
48	chr15:52806400-52806800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr15:52806400-52807000	Enhancers	Brain Substantia Nigra	brain
50	chr15:52806400-52809000	Enhancers	Skeletal Muscle Female	skeletal muscle

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