Variant report

Variant	rs17083326
Chromosome Location	chr4:54569479-54569480
allele	C/G
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	BCLAF1	chr4:54568668-54569520	GM12878	blood:	n/a	chr4:54569093-54569102 chr4:54568729-54568742
2	POLR2A	chr4:54568449-54569563	GM12878	blood:	n/a	n/a
3	TCF12	chr4:54568434-54569979	SK-N-SH	brain:	n/a	n/a
4	PAX5	chr4:54568582-54569575	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:54568268-54569546	GM19099	blood:	n/a	n/a
6	FOXM1	chr4:54568750-54569487	GM12878	blood:	n/a	n/a
7	CUX1	chr4:54568375-54569502	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:54568616-54569591	HUVEC	blood vessel:	n/a	n/a
9	STAT5A	chr4:54568925-54569488	GM12878	blood:	n/a	chr4:54569330-54569338
10	POLR2A	chr4:54568503-54569610	U87	brain:	n/a	n/a
11	MTA3	chr4:54568463-54569634	GM12878	blood:	n/a	n/a
12	NFIC	chr4:54568476-54569496	GM12878	blood:	n/a	chr4:54569290-54569307 chr4:54569291-54569307
13	RELA	chr4:54568515-54569491	GM10847	blood:	n/a	n/a
14	YY1	chr4:54568498-54569709	SK-N-SH_RA	brain:	n/a	chr4:54568734-54568745
15	KAP1	chr4:54568463-54569568	U2OS	brain:	n/a	n/a
16	POLR2A	chr4:54568317-54569510	GM18505	blood:	n/a	n/a
17	STAT3	chr4:54568945-54569583	GM12878	blood:	n/a	chr4:54569330-54569338
18	NFIC	chr4:54568607-54569652	ECC-1	luminal epithelium:	n/a	chr4:54569290-54569307 chr4:54569291-54569307
19	NFIC	chr4:54568565-54569622	SK-N-SH	brain:	n/a	chr4:54569290-54569307 chr4:54569291-54569307
20	REST	chr4:54569089-54569501	SK-N-SH	brain:	n/a	n/a
21	RELA	chr4:54568573-54569585	GM18505	blood:	n/a	n/a
22	EBF1	chr4:54568416-54569716	GM12878	blood:	n/a	chr4:54569214-54569225 chr4:54569215-54569224 chr4:54569321-54569330 chr4:54569321-54569330 chr4:54569215-54569224 chr4:54569213-54569226 chr4:54569215-54569225 chr4:54569320-54569330
23	RELA	chr4:54568542-54569633	GM12891	blood:	n/a	n/a
24	KAP1	chr4:54568533-54569662	HEK293	kidney:	n/a	n/a
25	EP300	chr4:54568521-54569679	SK-N-SH	brain:	n/a	chr4:54568734-54568750 chr4:54569007-54569017
26	POLR2A	chr4:54568537-54569490	GM19193	blood:	n/a	n/a
27	EP300	chr4:54568677-54569784	SK-N-SH_RA	brain:	n/a	chr4:54568734-54568750 chr4:54569007-54569017
28	SP1	chr4:54568516-54569521	GM12878	blood:	n/a	chr4:54568641-54568648 chr4:54568962-54568974 chr4:54569331-54569345 chr4:54568963-54568973 chr4:54568963-54568972
29	EP300	chr4:54568459-54569770	SK-N-SH_RA	brain:	n/a	chr4:54568734-54568750 chr4:54569007-54569017
30	REST	chr4:54569102-54569499	A549	lung:	n/a	n/a
31	TBL1XR1	chr4:54568388-54569515	GM12878	blood:	n/a	n/a
32	MAX	chr4:54568610-54569550	A549	lung:	n/a	chr4:54569168-54569178
33	RUNX3	chr4:54568536-54569557	GM12878	blood:	n/a	n/a
34	EBF1	chr4:54568478-54569585	GM12878	blood:	n/a	chr4:54569214-54569225 chr4:54569215-54569224 chr4:54569321-54569330 chr4:54569321-54569330 chr4:54569215-54569224 chr4:54569213-54569226 chr4:54569215-54569225 chr4:54569320-54569330
35	TCF7L2	chr4:54568600-54569517	Hela-S3	cervix:	n/a	chr4:54569285-54569295
36	IRF4	chr4:54568542-54569498	GM12878	blood:	n/a	n/a
37	MAX	chr4:54568661-54569479	HepG2	liver:	n/a	chr4:54569168-54569178
38	BHLHE40	chr4:54568530-54569511	GM12878	blood:	n/a	n/a
39	MTA3	chr4:54568742-54569651	GM12878	blood:	n/a	n/a
40	RELA	chr4:54568452-54569502	GM12878	blood:	n/a	n/a
41	MAX	chr4:54568719-54569624	SK-N-SH	brain:	n/a	chr4:54569168-54569178
42	ELK1	chr4:54569269-54569491	Hela-S3	cervix:	n/a	n/a
43	GTF2F1	chr4:54568671-54569540	Hela-S3	cervix:	n/a	chr4:54568904-54568915
44	PBX3	chr4:54568480-54569629	SK-N-SH	brain:	n/a	n/a
45	RXRA	chr4:54568487-54569669	SK-N-SH	brain:	n/a	n/a
46	RCOR1	chr4:54568543-54569501	Hela-S3	cervix:	n/a	n/a
47	RELA	chr4:54568521-54569653	GM18951	blood:	n/a	n/a
48	POLR2A	chr4:54568625-54569551	U87	brain:	n/a	n/a
49	USF2	chr4:54569039-54569596	GM12878	blood:	n/a	n/a
50	RUNX3	chr4:54568499-54569617	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54568125..54570977-chr4:54571339..54573651,2	K562	blood:

Variant related genes	Relation type
LNX1	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17083344	0.82[AFR][1000 genomes]
rs17083355	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28459143	0.90[ASN][1000 genomes]
rs28484855	0.98[ASN][1000 genomes]
rs28589490	0.85[ASN][1000 genomes]
rs28613767	0.98[ASN][1000 genomes]
rs56753131	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60293431	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6844085	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs728587	0.98[ASN][1000 genomes]
rs7671090	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54568000-54569600	Flanking Active TSS	GM12878-XiMat	blood
2	chr4:54568000-54569800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr4:54568400-54569600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:54568400-54569600	Flanking Active TSS	Liver	Liver
5	chr4:54568400-54569600	Enhancers	Fetal Brain Male	brain
6	chr4:54568400-54569800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:54568400-54569800	Flanking Active TSS	Hela-S3	cervix
8	chr4:54568600-54569600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr4:54568600-54569600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr4:54568600-54569600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:54568600-54569600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:54568600-54569600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:54568600-54569600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:54568600-54569600	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr4:54568600-54569600	Enhancers	Gastric	stomach
16	chr4:54568600-54569600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr4:54568600-54569600	Flanking Active TSS	Right Atrium	heart
18	chr4:54568600-54569600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr4:54568600-54569600	Enhancers	Stomach Mucosa	stomach
20	chr4:54568600-54569600	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr4:54568600-54569600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr4:54568600-54569600	Flanking Active TSS	NH-A	brain
23	chr4:54568600-54569600	Flanking Active TSS	NHDF-Ad	bronchial
24	chr4:54568600-54569600	Flanking Active TSS	NHLF	lung
25	chr4:54568600-54569800	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr4:54568600-54569800	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr4:54568600-54569800	Enhancers	Placenta	Placenta
28	chr4:54568600-54569800	Enhancers	Fetal Thymus	thymus
29	chr4:54568600-54569800	Enhancers	Lung	lung
30	chr4:54568600-54569800	Enhancers	Spleen	Spleen
31	chr4:54568600-54569800	Flanking Active TSS	HUVEC	blood vessel
32	chr4:54568600-54569800	Flanking Active TSS	Osteobl	bone
33	chr4:54568600-54570000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:54568600-54570200	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr4:54568600-54570400	Enhancers	Fetal Stomach	stomach
36	chr4:54568800-54569600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr4:54568800-54569600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr4:54568800-54569800	Enhancers	H9 Cell Line	embryonic stem cell
39	chr4:54568800-54569800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:54568800-54569800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr4:54568800-54569800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:54568800-54570200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:54569000-54569600	Flanking Active TSS	Colonic Mucosa	Colon
44	chr4:54569000-54569600	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr4:54569000-54569600	Flanking Active TSS	Fetal Lung	lung
46	chr4:54569000-54569800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:54569000-54569800	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr4:54569000-54569800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:54569000-54569800	Enhancers	Fetal Intestine Large	intestine
50	chr4:54569000-54569800	Enhancers	Small Intestine	intestine

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