Variant report

Variant	rs1642933
Chromosome Location	chr15:57261065-57261066
allele	C/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	FOXA1	chr15:57260969-57261399	HepG2	liver:	n/a	chr15:57261288-57261303
2	FOXA2	chr15:57260967-57261538	A549	lung:	n/a	n/a
3	FOXA1	chr15:57261053-57261538	HepG2	liver:	n/a	chr15:57261288-57261303
4	FOXA1	chr15:57260995-57261427	HepG2	liver:	n/a	chr15:57261288-57261303

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57210057..57212896-chr15:57260738..57263139,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222586	TF binding region
ENSG00000137871	Chromatin interaction
ENSG00000140262	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1642932	0.84[AFR][1000 genomes]
rs1642938	0.85[AFR][1000 genomes]
rs1652734	0.91[AFR][1000 genomes]
rs1652735	0.91[AFR][1000 genomes]
rs213145	0.87[AFR][1000 genomes]
rs213146	0.87[AFR][1000 genomes]
rs213157	0.85[AFR][1000 genomes]
rs213159	0.87[AFR][1000 genomes]
rs213161	0.87[AFR][1000 genomes]
rs213169	0.87[AFR][1000 genomes]
rs604191	0.87[AFR][1000 genomes]
rs73411246	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv904250	chr15:57225766-57294085	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57256200-57263400	Weak transcription	Lung	lung
2	chr15:57256200-57264400	Weak transcription	NH-A	brain
3	chr15:57256200-57265200	Weak transcription	Fetal Brain Male	brain
4	chr15:57256200-57265800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:57256400-57261400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:57256400-57263600	Weak transcription	Brain Germinal Matrix	brain
7	chr15:57256400-57264000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr15:57256400-57265200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr15:57256800-57263000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr15:57256800-57263600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr15:57256800-57263600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:57256800-57264400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:57256800-57277200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr15:57257200-57264600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:57257200-57274600	Weak transcription	Adipose Nuclei	Adipose
16	chr15:57257400-57263600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:57257800-57265400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr15:57258000-57263600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:57258200-57264000	Weak transcription	NHDF-Ad	bronchial
20	chr15:57259200-57261200	Enhancers	Right Atrium	heart
21	chr15:57259400-57261800	Enhancers	Primary T cells from cord blood	blood
22	chr15:57259400-57262000	Enhancers	Brain Substantia Nigra	brain
23	chr15:57259400-57262200	Enhancers	Brain Hippocampus Middle	brain
24	chr15:57259400-57262400	Enhancers	Liver	Liver
25	chr15:57259400-57262400	Enhancers	A549	lung
26	chr15:57259400-57268200	Enhancers	HepG2	liver
27	chr15:57259600-57261200	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr15:57259600-57261200	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr15:57259600-57261200	Enhancers	Right Ventricle	heart
30	chr15:57259600-57261400	Enhancers	Brain Cingulate Gyrus	brain
31	chr15:57259600-57262000	Enhancers	Brain Anterior Caudate	brain
32	chr15:57259600-57262200	Enhancers	Thymus	Thymus
33	chr15:57259800-57261200	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr15:57259800-57264600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr15:57260000-57263800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr15:57260000-57272200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:57260000-57272400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr15:57260200-57261200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr15:57260200-57262000	Enhancers	Pancreas	Pancrea
40	chr15:57260200-57263800	Weak transcription	Fetal Heart	heart
41	chr15:57260400-57261200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr15:57260400-57261400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr15:57260400-57262200	Enhancers	Small Intestine	intestine
44	chr15:57260600-57261200	Enhancers	H1 Cell Line	embryonic stem cell
45	chr15:57260600-57261200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:57260600-57261200	Enhancers	H9 Cell Line	embryonic stem cell
47	chr15:57260600-57261200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr15:57260600-57261200	Enhancers	Gastric	stomach
49	chr15:57260600-57261200	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr15:57260600-57261400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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