Variant report

Variant	rs28534747
Chromosome Location	chr15:40374269-40374270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:112)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:112 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RXRA	chr15:40373727-40374332	HepG2	liver:	n/a	n/a
2	MBD4	chr15:40373698-40374376	HepG2	liver:	n/a	n/a
3	SP1	chr15:40373815-40374371	HepG2	liver:	n/a	n/a
4	CTCF	chr15:40374120-40374270	HVMF	connective:	n/a	n/a
5	FOXA1	chr15:40373711-40374316	HepG2	liver:	n/a	n/a
6	RAD21	chr15:40373890-40374370	IMR90	lung:	n/a	n/a
7	MAZ	chr15:40373812-40374386	HepG2	liver:	n/a	n/a
8	MXI1	chr15:40373850-40374991	HepG2	liver:	n/a	n/a
9	RAD21	chr15:40373876-40374298	SK-N-SH_RA	brain:	n/a	n/a
10	GATA1	chr15:40372514-40374402	K562	blood:	n/a	chr15:40373145-40373166 chr15:40372880-40372889 chr15:40373220-40373229 chr15:40372927-40372934
11	POLR2A	chr15:40373890-40374272	IMR90	lung:	n/a	n/a
12	YY1	chr15:40373823-40374348	HepG2	liver:	n/a	n/a
13	ARID3A	chr15:40373815-40374321	HepG2	liver:	n/a	n/a
14	CTCF	chr15:40374140-40374290	BE2_C	brain:	n/a	n/a
15	MYC	chr15:40372818-40374377	K562	blood:	n/a	n/a
16	NFIC	chr15:40373778-40374352	HepG2	liver:	n/a	chr15:40373950-40373978
17	JUND	chr15:40373932-40374345	HepG2	liver:	n/a	chr15:40374123-40374132
18	CTCF	chr15:40374078-40374294	IMR90	lung:	n/a	n/a
19	CHD2	chr15:40374051-40374292	GM12878	blood:	n/a	n/a
20	SMC3	chr15:40373747-40374504	HepG2	liver:	n/a	n/a
21	RAD21	chr15:40373925-40374288	HepG2	liver:	n/a	n/a
22	RCOR1	chr15:40373826-40374270	K562	blood:	n/a	n/a
23	HEY1	chr15:40373683-40374410	HepG2	liver:	n/a	n/a
24	CTCF	chr15:40374140-40374290	HEK293	kidney:	n/a	n/a
25	POLR2A	chr15:40373702-40374433	HUVEC	blood vessel:	n/a	n/a
26	CTCF	chr15:40374140-40374290	GM06990	blood:	n/a	n/a
27	EP300	chr15:40373731-40374383	HepG2	liver:	n/a	n/a
28	MYBL2	chr15:40373560-40374402	HepG2	liver:	n/a	n/a
29	POLR2A	chr15:40373908-40374363	K562	blood:	n/a	n/a
30	CTCF	chr15:40374040-40374310	GM12866	blood:	n/a	n/a
31	MAX	chr15:40373932-40374381	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr15:40373980-40374270	HCM	heart:	n/a	n/a
33	CTCF	chr15:40374240-40374390	GM12872	blood:	n/a	n/a
34	MAX	chr15:40373835-40374329	SK-N-SH	brain:	n/a	n/a
35	TCF12	chr15:40373821-40374269	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr15:40372535-40375358	HepG2	liver:	n/a	n/a
37	EP300	chr15:40373679-40374377	HepG2	liver:	n/a	n/a
38	USF1	chr15:40373803-40374278	HCT-116	colon:	n/a	chr15:40374049-40374060
39	MXI1	chr15:40373595-40374862	IMR90	lung:	n/a	n/a
40	RCOR1	chr15:40373853-40375276	HepG2	liver:	n/a	n/a
41	USF1	chr15:40373807-40374281	SK-N-SH_RA	brain:	n/a	chr15:40374049-40374060
42	FOXA2	chr15:40373794-40374273	HepG2	liver:	n/a	n/a
43	POLR2A	chr15:40372779-40375112	HUVEC	blood vessel:	n/a	n/a
44	CTCF	chr15:40374120-40374270	HepG2	liver:	n/a	n/a
45	RCOR1	chr15:40374001-40374495	K562	blood:	n/a	n/a
46	USF2	chr15:40373960-40374405	GM12878	blood:	n/a	n/a
47	CTCF	chr15:40374160-40374310	SK-N-SH_RA	brain:	n/a	n/a
48	FOXA1	chr15:40373756-40374338	HepG2	liver:	n/a	n/a
49	MAFK	chr15:40373938-40374289	K562	blood:	n/a	n/a
50	CTCF	chr15:40374120-40374270	HRPEpiC	eye:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40372039..40375867-chr15:40386826..40392262,4	K562	blood:
2	chr15:40373200..40375789-chr15:40377087..40378964,2	MCF-7	breast:
3	chr15:40372710..40375354-chr15:40380441..40382230,2	K562	blood:
4	chr15:40372535..40375363-chr15:40378032..40381941,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000259584	TF binding region
ENSG00000259409	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11638521	0.87[EUR][1000 genomes]
rs28479712	0.89[EUR][1000 genomes]
rs28587891	0.89[EUR][1000 genomes]
rs28620926	0.88[EUR][1000 genomes]
rs4923852	0.83[EUR][1000 genomes]
rs4924415	0.87[EUR][1000 genomes]
rs4924416	0.88[EUR][1000 genomes]
rs7181230	0.88[EUR][1000 genomes]
rs7183977	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9972424	0.89[EUR][1000 genomes]
rs9972442	0.86[EUR][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	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40364800-40376800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:40372400-40376400	Enhancers	Fetal Heart	heart
3	chr15:40372800-40374800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:40372800-40375000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr15:40372800-40377000	Enhancers	Hela-S3	cervix
6	chr15:40373000-40374400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr15:40373000-40374400	Flanking Active TSS	HUVEC	blood vessel
8	chr15:40373000-40374600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:40373000-40374600	Flanking Active TSS	K562	blood
10	chr15:40373000-40374800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:40373000-40374800	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr15:40373000-40374800	Flanking Active TSS	Thymus	Thymus
13	chr15:40373000-40375400	Flanking Active TSS	GM12878-XiMat	blood
14	chr15:40373000-40376400	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr15:40373200-40374400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:40373200-40374400	Active TSS	Right Atrium	heart
17	chr15:40373200-40374600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:40373200-40374800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr15:40373400-40374400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:40373400-40374600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:40373600-40374400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:40373600-40374400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr15:40373600-40374400	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr15:40373600-40374400	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr15:40373600-40374400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr15:40373600-40374400	Flanking Active TSS	Fetal Intestine Small	intestine
27	chr15:40373600-40374400	Active TSS	Right Ventricle	heart
28	chr15:40373600-40374600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:40373600-40374600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:40373600-40374600	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr15:40373600-40374800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
32	chr15:40373600-40374800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr15:40373600-40374800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr15:40373600-40375000	Flanking Active TSS	Liver	Liver
35	chr15:40373600-40375200	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr15:40373800-40374400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:40373800-40374400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
38	chr15:40373800-40374400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
39	chr15:40373800-40374400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr15:40373800-40374400	Active TSS	Aorta	Aorta
41	chr15:40373800-40374400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr15:40373800-40374400	Flanking Active TSS	Fetal Intestine Large	intestine
43	chr15:40373800-40374400	Flanking Active TSS	Fetal Kidney	kidney
44	chr15:40373800-40374400	Flanking Active TSS	Fetal Lung	lung
45	chr15:40373800-40374400	Flanking Active TSS	Fetal Muscle Leg	muscle
46	chr15:40373800-40374400	Flanking Active TSS	NH-A	brain
47	chr15:40373800-40374600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
48	chr15:40373800-40374600	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
49	chr15:40373800-40374600	Flanking Active TSS	HSMM	muscle
50	chr15:40373800-40375000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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