Variant report

Variant	rs7659053
Chromosome Location	chr4:56414071-56414072
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	MYC	chr4:56413872-56414109	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr4:56414066-56414123	ProgFib	skin:	n/a	n/a
3	GATA3	chr4:56413889-56414149	SH-SY5Y	brain:	n/a	chr4:56413892-56413902
4	MAZ	chr4:56411530-56414133	IMR90	lung:	n/a	n/a
5	MXI1	chr4:56411663-56414396	IMR90	lung:	n/a	n/a
6	POLR2A	chr4:56412798-56414097	U87	brain:	n/a	n/a
7	MYC	chr4:56413918-56414112	MCF10A-Er-Src	breast:	n/a	n/a
8	MAFF	chr4:56413877-56414455	K562	blood:	n/a	chr4:56414273-56414291
9	MXI1	chr4:56410957-56414953	SK-N-SH	brain:	n/a	n/a
10	NRF1	chr4:56412670-56414120	SK-N-SH	brain:	n/a	chr4:56413156-56413165 chr4:56413056-56413070 chr4:56413153-56413167 chr4:56412875-56412889 chr4:56412878-56412892 chr4:56413059-56413070 chr4:56412880-56412889 chr4:56412878-56412887 chr4:56412878-56412889 chr4:56413156-56413167 chr4:56413059-56413068
11	MAX	chr4:56412501-56414109	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr4:56414038-56414101	MCF10A-Er-Src	breast:	n/a	n/a
13	MAX	chr4:56411740-56414149	A549	lung:	n/a	n/a
14	STAT3	chr4:56413940-56414116	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56260988..56264413-chr4:56410743..56414640,3	K562	blood:
2	chr4:56412329..56414161-chr4:56494486..56496762,2	K562	blood:
3	chr4:56275450..56278290-chr4:56412391..56414503,2	K562	blood:
4	chr4:56408119..56414507-chr4:56501105..56505595,8	K562	blood:

Variant related genes	Relation type
CLOCK	TF binding region
ENSG00000109255	Chromatin interaction
ENSG00000249700	Chromatin interaction
ENSG00000203615	Chromatin interaction
ENSG00000134851	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1047343	1.00[AMR][1000 genomes]
rs10517345	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11727248	0.95[AFR][1000 genomes]
rs1552522	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17085783	1.00[AMR][1000 genomes]
rs17085803	1.00[AMR][1000 genomes]
rs17085857	1.00[AMR][1000 genomes]
rs17085864	1.00[AMR][1000 genomes]
rs17085882	1.00[AMR][1000 genomes]
rs17085885	1.00[AMR][1000 genomes]
rs2412650	1.00[AMR][1000 genomes]
rs34028624	1.00[AMR][1000 genomes]
rs34822003	1.00[AMR][1000 genomes]
rs58578647	1.00[AMR][1000 genomes]
rs73151822	1.00[AMR][1000 genomes]
rs73151893	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73153621	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73153661	1.00[AMR][1000 genomes]
rs73153688	1.00[AMR][1000 genomes]
rs73816271	1.00[AMR][1000 genomes]
rs73816274	1.00[AMR][1000 genomes]
rs7657206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7661096	1.00[AMR][1000 genomes]
rs7662129	1.00[AMR][1000 genomes]
rs7663749	1.00[AMR][1000 genomes]
rs7680836	0.92[AFR][1000 genomes]
rs7686016	1.00[AMR][1000 genomes]
rs7696080	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3439567	chr4:56411220-56414568	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56410800-56414200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:56410800-56414200	Active TSS	NHLF	lung
3	chr4:56411000-56414200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:56411000-56414200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:56411000-56414200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr4:56411000-56414400	Active TSS	Fetal Brain Female	brain
7	chr4:56411200-56414400	Active TSS	Brain Germinal Matrix	brain
8	chr4:56411200-56414600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr4:56411400-56414200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:56411400-56414200	Active TSS	Fetal Muscle Leg	muscle
11	chr4:56411400-56414200	Active TSS	Fetal Stomach	stomach
12	chr4:56411600-56414200	Active TSS	Aorta	Aorta
13	chr4:56411600-56414400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:56411600-56414400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:56413200-56414200	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr4:56413200-56415000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr4:56413400-56414200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr4:56413400-56414200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr4:56413400-56414200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:56413400-56414200	Flanking Active TSS	Liver	Liver
21	chr4:56413400-56414200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr4:56413400-56414200	Flanking Active TSS	HUVEC	blood vessel
23	chr4:56413600-56414200	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr4:56413600-56414200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr4:56413600-56414200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr4:56413600-56414200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr4:56413600-56414200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr4:56413600-56414200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:56413600-56414200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr4:56413600-56414400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:56413600-56414400	Flanking Active TSS	HMEC	breast
32	chr4:56413600-56414400	Flanking Active TSS	NHEK	skin
33	chr4:56413600-56414600	Flanking Active TSS	Dnd41	blood
34	chr4:56413600-56414600	Flanking Active TSS	Osteobl	bone
35	chr4:56413800-56414200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:56413800-56414200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
37	chr4:56413800-56414200	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr4:56413800-56414200	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr4:56413800-56414200	Flanking Active TSS	Brain Hippocampus Middle	brain
40	chr4:56413800-56414200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr4:56413800-56414200	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr4:56413800-56414200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr4:56413800-56414200	Flanking Active TSS	Fetal Heart	heart
44	chr4:56413800-56414200	Flanking Active TSS	Fetal Intestine Large	intestine
45	chr4:56413800-56414200	Flanking Active TSS	Fetal Lung	lung
46	chr4:56413800-56414200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr4:56413800-56414200	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr4:56413800-56414200	Flanking Active TSS	Hela-S3	cervix
49	chr4:56413800-56414200	Flanking Active TSS	HSMM	muscle
50	chr4:56413800-56414200	Flanking Active TSS	NH-A	brain

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