Variant report

Variant	rs1550439
Chromosome Location	chr15:74221639-74221640
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr15:74217976-74222304	IMR90	lung:	n/a	n/a
2	POLR2A	chr15:74221179-74221725	MCF-7	breast:	n/a	n/a
3	POLR2A	chr15:74217872-74240199	U87	brain:	n/a	n/a
4	POLR2A	chr15:74215819-74242527	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:74163735..74170089-chr15:74218002..74222715,6	MCF-7	breast:
2	chr15:74190385..74192621-chr15:74220750..74222967,2	MCF-7	breast:
3	chr15:74220838..74222691-chr15:74242303..74245094,2	MCF-7	breast:

Variant related genes	Relation type
LOXL1-AS1	TF binding region
ENSG00000260624	Chromatin interaction
ENSG00000167139	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12594324	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1440101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16958494	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304721	0.95[ASN][1000 genomes]
rs28603291	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41435250	0.87[ASN][1000 genomes]
rs58490364	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73446383	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs893815	0.82[AFR][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	nsv1043335	chr15:74078689-74241186	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1603	chr15:74191222-74235733	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2758387	chr15:74215114-74464916	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv2760040	chr15:74215114-74464916	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv428308	chr15:74215114-74464916	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74218800-74221800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr15:74220200-74221800	Enhancers	Spleen	Spleen
3	chr15:74220400-74221800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:74220400-74222600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:74220400-74222800	Enhancers	Fetal Heart	heart
6	chr15:74220400-74223400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr15:74220400-74223400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:74220600-74221800	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr15:74220600-74222000	Enhancers	Left Ventricle	heart
10	chr15:74220600-74222200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:74220600-74222600	Weak transcription	Ovary	ovary
12	chr15:74220600-74223400	Enhancers	Placenta	Placenta
13	chr15:74220800-74221800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr15:74220800-74221800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:74220800-74221800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:74220800-74221800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr15:74220800-74221800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr15:74220800-74221800	Enhancers	Duodenum Mucosa	Duodenum
19	chr15:74220800-74221800	Bivalent Enhancer	Fetal Stomach	stomach
20	chr15:74220800-74222000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
21	chr15:74220800-74222000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr15:74220800-74222000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr15:74220800-74222000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr15:74220800-74222000	Bivalent Enhancer	Colon Smooth Muscle	Colon
25	chr15:74220800-74222000	Enhancers	Stomach Mucosa	stomach
26	chr15:74220800-74222200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr15:74220800-74222200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:74220800-74222200	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr15:74220800-74222200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr15:74220800-74222200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:74220800-74222200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:74220800-74222200	Weak transcription	Esophagus	oesophagus
33	chr15:74220800-74222200	Weak transcription	HMEC	breast
34	chr15:74220800-74222200	Weak transcription	NHEK	skin
35	chr15:74220800-74222400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:74220800-74222400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:74220800-74222400	Weak transcription	Colonic Mucosa	Colon
38	chr15:74220800-74222400	Enhancers	Fetal Thymus	thymus
39	chr15:74220800-74222800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:74220800-74223200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr15:74220800-74223200	Enhancers	Right Ventricle	heart
42	chr15:74220800-74223400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr15:74220800-74224200	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr15:74220800-74224800	Weak transcription	Hela-S3	cervix
45	chr15:74220800-74226000	Weak transcription	Pancreas	Pancrea
46	chr15:74220800-74226200	Weak transcription	Lung	lung
47	chr15:74220800-74228000	Weak transcription	Fetal Kidney	kidney
48	chr15:74220800-74228400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr15:74221000-74222000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr15:74221000-74223600	Enhancers	Brain Germinal Matrix	brain

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