Variant report

Variant	rs28578651
Chromosome Location	chr15:52812759-52812760
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52799417..52803271-chr15:52809477..52812870,3	MCF-7	breast:
2	chr15:52807587..52810925-chr15:52812381..52815095,4	MCF-7	breast:
3	chr15:52807642..52810251-chr15:52810841..52812773,2	K562	blood:
4	chr15:52812726..52818760-chr15:52818912..52822448,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197535	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

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	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	0.92[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	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28570350	0.87[ASN][1000 genomes]
rs28581262	1.00[ASN][1000 genomes]
rs28589619	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28642806	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28649737	1.00[AMR][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	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28711556	0.96[AFR][1000 genomes]
rs28761013	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28786736	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28787300	0.88[AFR][1000 genomes]
rs28795685	0.86[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	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28840839	0.87[ASN][1000 genomes]
rs28876722	0.87[ASN][1000 genomes]
rs3764226	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	0.92[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:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52792000-52815200	Weak transcription	NHLF	lung
2	chr15:52796800-52819400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr15:52796800-52820000	Weak transcription	Primary T cells from cord blood	blood
4	chr15:52797000-52815200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:52797600-52819800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr15:52803800-52814800	Weak transcription	NHDF-Ad	bronchial
7	chr15:52804000-52814000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:52807000-52814200	Weak transcription	Brain Substantia Nigra	brain
9	chr15:52807400-52814000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:52807400-52820200	Weak transcription	Lung	lung
11	chr15:52807800-52816800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr15:52807800-52819800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:52808000-52815200	Weak transcription	HUVEC	blood vessel
14	chr15:52809000-52814600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:52809000-52815400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:52809600-52814800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:52809600-52814800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr15:52809600-52815200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:52810000-52814800	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr15:52810800-52813800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:52810800-52815000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:52810800-52815200	Weak transcription	A549	lung
23	chr15:52811000-52813600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:52811200-52815000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr15:52811400-52813400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr15:52811400-52813600	Weak transcription	NHEK	skin
27	chr15:52811400-52813800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:52811400-52814800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:52811400-52814800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:52811400-52816400	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr15:52811600-52812800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr15:52811600-52817400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr15:52811600-52817600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr15:52811600-52819400	Weak transcription	Primary B cells from cord blood	blood
35	chr15:52812000-52812800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:52812000-52812800	Enhancers	Psoas Muscle	Psoas
37	chr15:52812000-52812800	Enhancers	Right Atrium	heart
38	chr15:52812200-52812800	Enhancers	Brain Angular Gyrus	brain
39	chr15:52812200-52812800	Enhancers	Brain Cingulate Gyrus	brain
40	chr15:52812200-52812800	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr15:52812200-52813000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr15:52812200-52814000	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr15:52812400-52812800	Enhancers	Primary B cells from peripheral blood	blood
44	chr15:52812400-52812800	Enhancers	Brain Anterior Caudate	brain
45	chr15:52812400-52812800	Enhancers	Colon Smooth Muscle	Colon
46	chr15:52812400-52812800	Enhancers	Left Ventricle	heart
47	chr15:52812400-52812800	Enhancers	Spleen	Spleen
48	chr15:52812400-52812800	Enhancers	HSMMtube	muscle
49	chr15:52812400-52813000	Enhancers	Adipose Nuclei	Adipose
50	chr15:52812400-52813000	Enhancers	Brain Inferior Temporal Lobe	brain

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