Variant report

Variant	rs28390245
Chromosome Location	chr15:40453058-40453059
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	SP1	chr15:40452838-40453723	HCT-116	colon:	n/a	chr15:40453210-40453220 chr15:40453475-40453489 chr15:40453264-40453274 chr15:40453209-40453221 chr15:40453209-40453221 chr15:40453210-40453220
2	SIX5	chr15:40452821-40453378	K562	blood:	n/a	chr15:40453108-40453122 chr15:40453112-40453121 chr15:40453110-40453119 chr15:40453107-40453116 chr15:40453157-40453171
3	POLR2A	chr15:40452979-40453925	GM12878	blood:	n/a	n/a
4	EP300	chr15:40453012-40453320	T-47D	breast:	n/a	n/a
5	ARID3A	chr15:40453023-40453412	HepG2	liver:	n/a	n/a
6	POLR2A	chr15:40453004-40453825	Hela-S3	cervix:	n/a	n/a
7	MAX	chr15:40452979-40453859	K562	blood:	n/a	chr15:40453636-40453647
8	MYC	chr15:40453041-40453363	MCF10A-Er-Src	breast:	n/a	n/a
9	ZNF143	chr15:40452869-40453564	Hela-S3	cervix:	n/a	chr15:40453110-40453119 chr15:40453163-40453182 chr15:40453112-40453121 chr15:40453159-40453177 chr15:40453117-40453132 chr15:40453110-40453128
10	POLR2A	chr15:40452915-40453565	HUVEC	blood vessel:	n/a	n/a
11	BRCA1	chr15:40452990-40453370	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:40452807-40453746	HepG2	liver:	n/a	n/a
13	MYC	chr15:40453040-40453472	HepG2	liver:	n/a	n/a
14	POLR2A	chr15:40453040-40453588	GM12892	blood:	n/a	n/a
15	USF2	chr15:40452885-40453291	GM12878	blood:	n/a	n/a
16	BRCA1	chr15:40452763-40453470	Hela-S3	cervix:	n/a	n/a
17	ELF1	chr15:40452833-40453542	GM12878	blood:	n/a	n/a
18	MAFF	chr15:40452992-40453284	K562	blood:	n/a	n/a
19	E2F4	chr15:40452994-40453498	GM12878	blood:	n/a	n/a
20	MYC	chr15:40452957-40453920	K562	blood:	n/a	chr15:40453636-40453647
21	POLR2A	chr15:40453054-40453719	GM12878	blood:	n/a	n/a
22	ETS1	chr15:40452966-40453601	K562	blood:	n/a	chr15:40453109-40453122 chr15:40453158-40453171
23	WRNIP1	chr15:40452919-40453363	GM12878	blood:	n/a	n/a
24	MAX	chr15:40452939-40453944	Hela-S3	cervix:	n/a	chr15:40453636-40453647
25	CREB1	chr15:40452791-40453777	HepG2	liver:	n/a	n/a
26	ETS1	chr15:40452889-40453448	GM12878	blood:	n/a	chr15:40453109-40453122 chr15:40453158-40453171
27	POLR2A	chr15:40453029-40453519	MCF10A-Er-Src	breast:	n/a	n/a
28	SMC3	chr15:40452715-40453354	HepG2	liver:	n/a	n/a
29	PML	chr15:40452762-40453724	GM12878	blood:	n/a	n/a
30	FOXA2	chr15:40452887-40453491	A549	lung:	n/a	n/a
31	SIN3AK20	chr15:40452775-40453855	HCT-116	colon:	n/a	n/a
32	GABPA	chr15:40452910-40453390	A549	lung:	n/a	n/a
33	BRCA1	chr15:40452984-40453787	H1-hESC	embryonic stem cell:	n/a	n/a
34	FOXA1	chr15:40452842-40453336	T-47D	breast:	n/a	n/a
35	NFIC	chr15:40452932-40453696	ECC-1	luminal epithelium:	n/a	n/a
36	SIX5	chr15:40452850-40453477	A549	lung:	n/a	chr15:40453108-40453122 chr15:40453112-40453121 chr15:40453110-40453119 chr15:40453107-40453116 chr15:40453157-40453171
37	MAX	chr15:40452907-40453869	H1-hESC	embryonic stem cell:	n/a	chr15:40453636-40453647
38	PAX5	chr15:40452990-40453472	GM12892	blood:	n/a	n/a
39	MAFK	chr15:40453003-40453280	HepG2	liver:	n/a	n/a
40	YY1	chr15:40452938-40453476	HCT-116	colon:	n/a	n/a
41	ZNF384	chr15:40452993-40453447	K562	blood:	n/a	n/a
42	RXRA	chr15:40452853-40453402	GM12878	blood:	n/a	n/a
43	ZBTB33	chr15:40453010-40453313	HepG2	liver:	n/a	chr15:40453230-40453240
44	PAX5	chr15:40453040-40453324	GM12878	blood:	n/a	n/a
45	STAT3	chr15:40452842-40453345	GM12878	blood:	n/a	n/a
46	MAX	chr15:40452967-40453850	K562	blood:	n/a	chr15:40453636-40453647
47	TEAD4	chr15:40452917-40453999	H1-hESC	embryonic stem cell:	n/a	n/a
48	GTF2F1	chr15:40452844-40453496	Hela-S3	cervix:	n/a	n/a
49	TAF1	chr15:40452893-40453849	ECC-1	luminal epithelium:	n/a	n/a
50	PAX5	chr15:40452897-40453536	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:40453034-40453084	MCF-7	breast:	n/a
2	chr15:40453034-40453084	BE2_C	brain:	n/a
3	chr15:40453036-40453086	NT2-D1	testis:	n/a
4	chr15:40453034-40453084	HEK293	kidney:	embryo
5	chr15:40453036-40453086	HCT-116	colon:	n/a
6	chr15:40453036-40453086	HCF	heart:	n/a
7	chr15:40453034-40453084	RPTEC	kidney:	n/a
8	chr15:40453036-40453086	PrEC	prostate:	n/a
9	chr15:40453034-40453084	HRPEpiC	eye:	n/a
10	chr15:40453034-40453084	HPAEpiC	pulmonary alveolar:	n/a
11	chr15:40453034-40453084	NT2-D1	testis:	n/a
12	chr15:40453036-40453086	GM19239	blood:	n/a
13	chr15:40453034-40453084	H1-hESC	embryonic stem cell:	embryo
14	chr15:40453036-40453086	AG09309	skin:	n/a
15	chr15:40453036-40453086	ECC-1	luminal epithelium:	n/a
16	chr15:40453034-40453084	SKMC	muscle:	n/a
17	chr15:40453036-40453086	Jurkat	blood:	n/a
18	chr15:40453036-40453086	HRCEpiC	kidney:	n/a
19	chr15:40453036-40453086	SK-N-MC	brain:	n/a
20	chr15:40453034-40453084	SK-N-MC	brain:	n/a
21	chr15:40453036-40453086	GM06990	blood:	n/a
22	chr15:40453034-40453084	HL-60	blood:	n/a
23	chr15:40453034-40453084	SK-N-SH	brain:	n/a
24	chr15:40453036-40453086	GM12878	blood:	n/a
25	chr15:40453036-40453086	HepG2	liver:	n/a
26	chr15:40453034-40453084	Hepatocyte	liver:	n/a
27	chr15:40453036-40453086	AG09319	gingival:	n/a
28	chr15:40453034-40453084	HEEpiC	esophagus:	n/a
29	chr15:40453034-40453084	GM12891	blood:	n/a
30	chr15:40453036-40453086	HPAEpiC	pulmonary alveolar:	n/a
31	chr15:40453036-40453086	HMEC	breast:	n/a
32	chr15:40453034-40453084	PrEC	prostate:	n/a
33	chr15:40453036-40453086	ProgFib	skin:	n/a
34	chr15:40453036-40453086	HEK293	kidney:	embryo
35	chr15:40453034-40453084	LNCaP	prostate:	n/a
36	chr15:40453036-40453086	GM12892	blood:	n/a
37	chr15:40453036-40453086	AG10803	skin:	n/a
38	chr15:40453034-40453084	BJ	skin:	n/a
39	chr15:40453034-40453084	PANC-1	pancreas:	n/a
40	chr15:40453034-40453084	HCM	heart:	n/a
41	chr15:40453034-40453084	HCT-116	colon:	n/a
42	chr15:40453036-40453086	HEEpiC	esophagus:	n/a
43	chr15:40453034-40453084	IMR90	lung:	fetal
44	chr15:40453034-40453084	Jurkat	blood:	n/a
45	chr15:40453034-40453084	Caco-2	colon:	n/a
46	chr15:40453034-40453084	U87	brain:	n/a
47	chr15:40453036-40453086	HRPEpiC	eye:	n/a
48	chr15:40453034-40453084	SK-N-SH_RA	brain:	n/a
49	chr15:40453036-40453086	HCPEpiC	choroid plexus:	n/a
50	chr15:40453036-40453086	GM12891	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40401050..40404743-chr15:40451589..40454397,3	K562	blood:
2	chr15:40355705..40358626-chr15:40451633..40453971,2	K562	blood:
3	chr15:40399053..40404293-chr15:40451574..40455090,8	MCF-7	breast:
4	chr15:40452220..40455176-chr15:40475826..40477725,2	K562	blood:

Variant related genes	Relation type
BUB1B	TF binding region
BUB1B	CpG island
ENSG00000104081	Chromatin interaction
ENSG00000248508	Chromatin interaction
ENSG00000156970	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11070254	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070255	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12102172	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12385956	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13380113	1.00[EUR][1000 genomes]
rs13380241	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1494534	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1801528	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1869906	1.00[EUR][1000 genomes]
rs28417868	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28418337	0.87[AMR][1000 genomes]
rs28485685	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28501335	1.00[EUR][1000 genomes]
rs28526743	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28561898	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28565228	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28606396	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28637656	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28637697	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28657938	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28668026	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28673302	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28744626	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28750294	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28792493	1.00[EUR][1000 genomes]
rs28844897	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28869227	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35611758	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56888636	1.00[EUR][1000 genomes]
rs57029027	1.00[EUR][1000 genomes]
rs58216655	1.00[EUR][1000 genomes]
rs58355728	0.87[AMR][1000 genomes]
rs58584688	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60743501	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60889301	1.00[EUR][1000 genomes]
rs7164281	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168394	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168416	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7173239	1.00[EUR][1000 genomes]
rs7178873	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73377835	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389487	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389489	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389492	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389507	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389520	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389531	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389536	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73389540	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390146	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390155	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390162	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390167	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390168	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73390187	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73391309	0.87[AMR][1000 genomes]
rs73391316	0.87[AMR][1000 genomes]
rs73392641	1.00[EUR][1000 genomes]
rs8023956	1.00[EUR][1000 genomes]
rs8026988	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8364	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9672591	1.00[EUR][1000 genomes]
rs967945	0.87[AMR][1000 genomes]
rs9806126	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9806144	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40450800-40453200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:40452200-40453200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:40452600-40453200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:40452600-40453200	Enhancers	Spleen	Spleen
5	chr15:40452600-40453200	Flanking Active TSS	Dnd41	blood
6	chr15:40452600-40453400	Active TSS	Brain Angular Gyrus	brain
7	chr15:40452600-40453400	Active TSS	Monocytes-CD14+_RO01746	blood
8	chr15:40452600-40455000	Active TSS	A549	lung
9	chr15:40452600-40455800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:40452800-40453200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr15:40452800-40453200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:40452800-40453200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:40452800-40453200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:40452800-40453200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr15:40452800-40453200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:40452800-40453200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr15:40452800-40453200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:40452800-40453200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr15:40452800-40453200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:40452800-40453200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:40452800-40453200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:40452800-40453200	Flanking Active TSS	Colon Smooth Muscle	Colon
23	chr15:40452800-40453200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr15:40452800-40453200	Flanking Active TSS	Fetal Thymus	thymus
25	chr15:40452800-40453200	Enhancers	Gastric	stomach
26	chr15:40452800-40453200	Enhancers	Lung	lung
27	chr15:40452800-40453200	Enhancers	Ovary	ovary
28	chr15:40452800-40453200	Enhancers	Placenta Amnion	Placenta Amnion
29	chr15:40452800-40453200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr15:40452800-40453200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr15:40452800-40453200	Flanking Active TSS	Rectal Smooth Muscle	rectum
32	chr15:40452800-40453200	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr15:40452800-40453200	Active TSS	Stomach Smooth Muscle	stomach
34	chr15:40452800-40453400	Active TSS	Brain Germinal Matrix	brain
35	chr15:40452800-40453400	Active TSS	Brain Substantia Nigra	brain
36	chr15:40452800-40453400	Active TSS	Fetal Muscle Leg	muscle
37	chr15:40452800-40453600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr15:40452800-40453600	Flanking Active TSS	Liver	Liver
39	chr15:40452800-40453600	Active TSS	Brain Hippocampus Middle	brain
40	chr15:40452800-40453600	Active TSS	Psoas Muscle	Psoas
41	chr15:40452800-40453800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr15:40452800-40453800	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr15:40452800-40453800	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr15:40452800-40453800	Active TSS	Brain Anterior Caudate	brain
45	chr15:40452800-40453800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
46	chr15:40452800-40454000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr15:40452800-40454000	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr15:40452800-40454000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr15:40452800-40454000	Active TSS	HSMMtube	muscle
50	chr15:40452800-40454200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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