Variant report

Variant	rs57537959
Chromosome Location	chr15:40527781-40527782
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	SPI1	chr15:40527345-40527884	HL-60	blood:	n/a	chr15:40527564-40527577 chr15:40527567-40527576 chr15:40527678-40527687 chr15:40527591-40527604
2	USF2	chr15:40527709-40528014	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr15:40526936-40528154	SK-N-MC	brain:	n/a	n/a
4	USF2	chr15:40527734-40527949	Hela-S3	cervix:	n/a	n/a
5	USF2	chr15:40527726-40527909	K562	blood:	n/a	n/a
6	NFYB	chr15:40527771-40528034	Hela-S3	cervix:	n/a	chr15:40527863-40527877 chr15:40527865-40527875 chr15:40527860-40527875 chr15:40527863-40527876 chr15:40527863-40527878 chr15:40527863-40527878
7	USF1	chr15:40527733-40527972	GM12878	blood:	n/a	chr15:40527848-40527859
8	USF1	chr15:40527629-40527968	H1-hESC	embryonic stem cell:	n/a	chr15:40527848-40527859
9	USF1	chr15:40527700-40527914	A549	lung:	n/a	chr15:40527848-40527859
10	SPI1	chr15:40527406-40527807	GM12891	blood:	n/a	chr15:40527564-40527577 chr15:40527567-40527576 chr15:40527678-40527687 chr15:40527591-40527604
11	USF1	chr15:40527694-40527951	SK-N-SH_RA	brain:	n/a	chr15:40527848-40527859
12	USF1	chr15:40527616-40528012	A549	lung:	n/a	chr15:40527848-40527859
13	USF1	chr15:40527671-40528009	SK-N-SH	brain:	n/a	chr15:40527848-40527859
14	USF1	chr15:40527606-40528010	K562	blood:	n/a	chr15:40527848-40527859
15	ATF3	chr15:40527758-40527915	K562	blood:	n/a	n/a
16	USF1	chr15:40527598-40528081	H1-hESC	embryonic stem cell:	n/a	chr15:40527848-40527859
17	USF1	chr15:40527521-40528144	HCT-116	colon:	n/a	chr15:40527848-40527859
18	USF1	chr15:40527669-40528069	ECC-1	luminal epithelium:	n/a	chr15:40527848-40527859
19	USF1	chr15:40527640-40528030	K562	blood:	n/a	chr15:40527848-40527859
20	SPI1	chr15:40527429-40527798	GM12891	blood:	n/a	chr15:40527564-40527577 chr15:40527567-40527576 chr15:40527678-40527687 chr15:40527591-40527604
21	USF2	chr15:40527713-40527990	GM12878	blood:	n/a	n/a
22	USF1	chr15:40527747-40527915	HepG2	liver:	n/a	chr15:40527848-40527859
23	USF1	chr15:40527609-40527995	SK-N-SH_RA	brain:	n/a	chr15:40527848-40527859
24	NFYB	chr15:40527693-40528064	K562	blood:	n/a	chr15:40527863-40527877 chr15:40527865-40527875 chr15:40527860-40527875 chr15:40527863-40527876 chr15:40527721-40527731 chr15:40527863-40527878 chr15:40527863-40527878 chr15:40527722-40527734
25	MAX	chr15:40527238-40528025	NB4	blood:	n/a	n/a
26	NFYB	chr15:40527679-40528073	GM12878	blood:	n/a	chr15:40527863-40527877 chr15:40527865-40527875 chr15:40527860-40527875 chr15:40527863-40527876 chr15:40527721-40527731 chr15:40527863-40527878 chr15:40527863-40527878 chr15:40527722-40527734
27	MAX	chr15:40527719-40527939	H1-hESC	embryonic stem cell:	n/a	n/a
28	SPI1	chr15:40526974-40527933	HL-60	blood:	n/a	chr15:40527564-40527577 chr15:40527567-40527576 chr15:40527678-40527687 chr15:40527591-40527604
29	USF1	chr15:40527729-40527994	ECC-1	luminal epithelium:	n/a	chr15:40527848-40527859
30	POLR2A	chr15:40527552-40528030	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40526580..40529009-chr15:40601249..40602782,2	K562	blood:
2	chr15:40527496..40529447-chr15:40561736..40564505,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BUB1B-1	chr15:40525645-40528308	ENSG00000260648.1
2	lnc-BUB1B-1	chr15:40524283-40528308	ENSG00000260648.2

Variant related genes	Relation type
PAK6	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs28418337	0.93[AFR][1000 genomes]
rs28459035	1.00[ASN][1000 genomes]
rs58355728	0.83[AFR][1000 genomes]
rs73389489	0.83[AFR][1000 genomes]
rs73391309	0.99[AFR][1000 genomes]
rs73391316	0.99[AFR][1000 genomes]
rs967945	0.94[AFR][1000 genomes]

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	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv904095	chr15:40525430-40591570	Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40455400-40530400	Weak transcription	Fetal Brain Female	brain
2	chr15:40455600-40530400	Weak transcription	Brain Germinal Matrix	brain
3	chr15:40492800-40530800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr15:40513200-40531200	Weak transcription	NHDF-Ad	bronchial
5	chr15:40513400-40530800	Weak transcription	A549	lung
6	chr15:40515400-40530600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:40516200-40530600	Weak transcription	Fetal Intestine Large	intestine
8	chr15:40517200-40530200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr15:40518200-40528600	Weak transcription	HUVEC	blood vessel
10	chr15:40519400-40529000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr15:40522200-40528800	Weak transcription	NHLF	lung
12	chr15:40522200-40530000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:40522400-40528600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:40522400-40528800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr15:40522400-40530400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:40522400-40530400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:40522400-40531800	Weak transcription	Gastric	stomach
18	chr15:40523600-40530400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:40523800-40528600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:40524000-40529200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:40524200-40528000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:40524200-40528200	Enhancers	HMEC	breast
23	chr15:40524200-40528600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:40524400-40527800	Enhancers	K562	blood
25	chr15:40524400-40528200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:40524400-40530800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:40524600-40528000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:40524600-40528400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr15:40525200-40529200	Weak transcription	NH-A	brain
30	chr15:40525200-40530400	Weak transcription	Fetal Intestine Small	intestine
31	chr15:40525200-40530400	Weak transcription	Lung	lung
32	chr15:40525200-40530800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:40525200-40531000	Weak transcription	Brain Anterior Caudate	brain
34	chr15:40525200-40531200	Weak transcription	Right Atrium	heart
35	chr15:40525400-40530600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr15:40525400-40531200	Weak transcription	Adipose Nuclei	Adipose
37	chr15:40526000-40528000	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr15:40526200-40528000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:40526200-40530400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr15:40526400-40528000	Enhancers	GM12878-XiMat	blood
41	chr15:40526600-40528200	Enhancers	Primary B cells from cord blood	blood
42	chr15:40526600-40529600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr15:40526600-40530800	Weak transcription	Thymus	Thymus
44	chr15:40526800-40527800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:40526800-40527800	Enhancers	Hela-S3	cervix
46	chr15:40526800-40528000	Enhancers	Primary hematopoietic stem cells	blood
47	chr15:40526800-40528400	Enhancers	Primary B cells from peripheral blood	blood
48	chr15:40527000-40528000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr15:40527000-40528000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr15:40527000-40528000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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