Variant report

Variant	rs28760390
Chromosome Location	chr15:57308431-57308432
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57209364..57212331-chr15:57308276..57309947,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12101705	1.00[AMR][1000 genomes]
rs12903733	1.00[AMR][1000 genomes]
rs16977150	1.00[AMR][1000 genomes]
rs16977156	1.00[AMR][1000 genomes]
rs16977168	1.00[AMR][1000 genomes]
rs16977178	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16977180	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16977183	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16977196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16977206	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16977215	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16977236	1.00[AMR][1000 genomes]
rs2733189	1.00[AMR][1000 genomes]
rs28393473	0.83[AFR][1000 genomes]
rs28637784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28647446	1.00[AMR][1000 genomes]
rs28648947	1.00[AMR][1000 genomes]
rs28669321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28682280	1.00[AMR][1000 genomes]
rs28710916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28718703	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28790102	1.00[AMR][1000 genomes]
rs28807215	1.00[AMR][1000 genomes]
rs3111100	1.00[AMR][1000 genomes]
rs57498481	1.00[AMR][1000 genomes]
rs57637767	1.00[AMR][1000 genomes]
rs59225036	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8030618	0.88[AFR][1000 genomes];1.00[AMR][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	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57276200-57313400	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr15:57277000-57313400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:57282000-57315000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr15:57282200-57311000	Weak transcription	K562	blood
5	chr15:57282200-57315200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr15:57284200-57310800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:57286200-57312000	Weak transcription	HSMM	muscle
8	chr15:57286200-57314800	Weak transcription	Dnd41	blood
9	chr15:57286400-57309400	Weak transcription	Fetal Lung	lung
10	chr15:57289600-57315200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:57289600-57315600	Weak transcription	Fetal Muscle Leg	muscle
12	chr15:57289800-57315600	Weak transcription	Primary B cells from cord blood	blood
13	chr15:57294400-57311600	Weak transcription	GM12878-XiMat	blood
14	chr15:57295200-57313600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:57296000-57308800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:57296000-57308800	Weak transcription	Brain Hippocampus Middle	brain
17	chr15:57296400-57309400	Weak transcription	NHDF-Ad	bronchial
18	chr15:57296400-57310200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr15:57296600-57313200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:57297200-57316800	Weak transcription	Fetal Stomach	stomach
21	chr15:57299200-57316000	Weak transcription	Right Ventricle	heart
22	chr15:57299200-57317200	Weak transcription	Esophagus	oesophagus
23	chr15:57300200-57313800	Strong transcription	Fetal Thymus	thymus
24	chr15:57300400-57308800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:57303600-57317600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr15:57305000-57310800	Weak transcription	Spleen	Spleen
27	chr15:57305000-57311200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:57305000-57311800	Weak transcription	Aorta	Aorta
29	chr15:57305000-57312000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:57305000-57313400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:57305000-57313400	Weak transcription	Right Atrium	heart
32	chr15:57306200-57308800	Enhancers	Small Intestine	intestine
33	chr15:57306400-57310600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:57306400-57310600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr15:57306400-57312400	Enhancers	Placenta	Placenta
36	chr15:57306600-57308600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr15:57307000-57311600	Weak transcription	NHLF	lung
38	chr15:57307400-57309000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr15:57307400-57309400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:57307400-57309400	Enhancers	Colon Smooth Muscle	Colon
41	chr15:57307400-57309400	Enhancers	NHEK	skin
42	chr15:57307400-57309600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:57307400-57309800	Enhancers	HMEC	breast
44	chr15:57307400-57311000	Enhancers	Fetal Intestine Large	intestine
45	chr15:57307600-57309200	Enhancers	HepG2	liver
46	chr15:57307600-57309400	Strong transcription	Primary hematopoietic stem cells	blood
47	chr15:57307600-57309400	Enhancers	Liver	Liver
48	chr15:57307600-57309600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:57307600-57309800	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr15:57307600-57312200	Enhancers	Brain Anterior Caudate	brain

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