Variant report

Variant	rs28742572
Chromosome Location	chr17:38574947-38574948
allele	G/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	SREBP2	chr17:38571524-38575100	GM12878	blood:	n/a	n/a
2	POLR2A	chr17:38573294-38575037	HepG2	liver:	n/a	n/a
3	MAX	chr17:38573483-38574989	MCF-7	breast:	n/a	n/a
4	POLR2A	chr17:38573071-38574998	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr17:38573586-38575009	MCF-7	breast:	n/a	n/a
6	MAX	chr17:38573337-38574974	A549	lung:	n/a	n/a
7	SP1	chr17:38573307-38575033	HCT-116	colon:	n/a	chr17:38574687-38574696 chr17:38574685-38574697 chr17:38574300-38574321 chr17:38574685-38574697 chr17:38574686-38574696 chr17:38574686-38574696 chr17:38574686-38574695 chr17:38574686-38574695 chr17:38574316-38574327
8	POLR2A	chr17:38574569-38574983	MCF-7	breast:	n/a	n/a
9	SIN3AK20	chr17:38573282-38575088	MCF-7	breast:	n/a	n/a
10	MAX	chr17:38573278-38575050	A549	lung:	n/a	n/a
11	POLR2A	chr17:38574567-38575024	MCF-7	breast:	n/a	n/a
12	MXI1	chr17:38572784-38574999	SK-N-SH	brain:	n/a	n/a
13	SP1	chr17:38573541-38574976	A549	lung:	n/a	chr17:38574687-38574696 chr17:38574685-38574697 chr17:38574300-38574321 chr17:38574685-38574697 chr17:38574686-38574696 chr17:38574686-38574696 chr17:38574686-38574695 chr17:38574686-38574695 chr17:38574316-38574327
14	SP1	chr17:38573137-38574958	A549	lung:	n/a	chr17:38574687-38574696 chr17:38574685-38574697 chr17:38574300-38574321 chr17:38574685-38574697 chr17:38574686-38574696 chr17:38574686-38574696 chr17:38574686-38574695 chr17:38574686-38574695 chr17:38574316-38574327
15	POLR2A	chr17:38573551-38574957	Raji	blood:	n/a	n/a
16	POLR2A	chr17:38573379-38574950	PFSK-1	brain:	n/a	n/a
17	SP1	chr17:38573522-38574959	HCT-116	colon:	n/a	chr17:38574687-38574696 chr17:38574685-38574697 chr17:38574300-38574321 chr17:38574685-38574697 chr17:38574686-38574696 chr17:38574686-38574696 chr17:38574686-38574695 chr17:38574686-38574695 chr17:38574316-38574327

No.	Distal block	Cell Line	Cell type
1	chr17:38572047..38583621-chr17:38597341..38605150,24	MCF-7	breast:
2	chr17:38519063..38522724-chr17:38572084..38575827,4	K562	blood:
3	chr17:38574110..38575071-chr7:66309477..66310025,2	HCT-116	colon:
4	chr17:38472434..38475174-chr17:38574466..38576068,2	MCF-7	breast:
5	chr17:38573492..38575865-chr17:38596037..38598385,2	K562	blood:
6	chr17:38571221..38576195-chr17:38597437..38603899,8	K562	blood:
7	chr17:38465403..38467512-chr17:38572698..38575190,2	MCF-7	breast:
8	chr17:38518117..38522815-chr17:38572084..38576075,6	K562	blood:

Variant related genes	Relation type
TOP2A	TF binding region
ENSG00000230583	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000141753	Chromatin interaction
ENSG00000240125	Chromatin interaction
ENSG00000183153	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11867497	1.00[MEX][hapmap]
rs12937995	1.00[MEX][hapmap]
rs34300454	1.00[CHD][hapmap]
rs34530029	1.00[CHD][hapmap]
rs35163502	1.00[MEX][hapmap]
rs4135012	1.00[CHD][hapmap]
rs9895942	1.00[MEX][hapmap]
rs9913992	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv908223	chr17:38530799-38609187	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38572200-38575000	Active TSS	Fetal Brain Female	brain
2	chr17:38572600-38575000	Active TSS	Thymus	Thymus
3	chr17:38573000-38575000	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr17:38573200-38575000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:38573400-38575000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr17:38573600-38575000	Active TSS	Osteobl	bone
7	chr17:38573800-38575000	Active TSS	Primary T killer memory cells from peripheral blood	blood
8	chr17:38573800-38575000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr17:38573800-38575000	Active TSS	Colon Smooth Muscle	Colon
10	chr17:38573800-38576000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr17:38574000-38575000	Active TSS	Ovary	ovary
12	chr17:38574000-38575000	Active TSS	Rectal Smooth Muscle	rectum
13	chr17:38574400-38575000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr17:38574400-38575000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr17:38574400-38575000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr17:38574400-38575000	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr17:38574400-38575000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr17:38574400-38575000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr17:38574400-38575000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr17:38574400-38575000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr17:38574400-38575000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr17:38574400-38575000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr17:38574400-38575000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr17:38574400-38575000	Flanking Active TSS	Dnd41	blood
25	chr17:38574400-38575000	Flanking Active TSS	Hela-S3	cervix
26	chr17:38574400-38576600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr17:38574400-38576600	Flanking Active TSS	HepG2	liver
28	chr17:38574600-38575000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr17:38574600-38575000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr17:38574600-38575000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr17:38574600-38575000	Flanking Active TSS	Primary B cells from peripheral blood	blood
32	chr17:38574600-38575000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr17:38574600-38575000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr17:38574600-38575000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr17:38574600-38575000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr17:38574600-38575000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr17:38574600-38575000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr17:38574600-38575000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr17:38574600-38575000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr17:38574600-38575000	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr17:38574600-38575000	Flanking Active TSS	Brain Substantia Nigra	brain
42	chr17:38574600-38575000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr17:38574600-38575000	Flanking Active TSS	Fetal Intestine Small	intestine
44	chr17:38574600-38575000	Flanking Active TSS	Fetal Muscle Trunk	muscle
45	chr17:38574600-38575000	Flanking Active TSS	Fetal Muscle Leg	muscle
46	chr17:38574600-38575000	Flanking Active TSS	Placenta	Placenta
47	chr17:38574600-38575000	Flanking Active TSS	Fetal Stomach	stomach
48	chr17:38574600-38575000	Flanking Active TSS	Fetal Thymus	thymus
49	chr17:38574600-38575000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr17:38574600-38575000	Flanking Active TSS	Stomach Smooth Muscle	stomach

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