Variant report

Variant	rs60077509
Chromosome Location	chr4:54569226-54569227
allele	A/C
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	chr4:54568894-54569373	NB4	blood:	n/a	chr4:54569168-54569178
2	POLR2A	chr4:54568809-54569273	HUVEC	blood vessel:	n/a	n/a
3	MEF2A	chr4:54568781-54569408	GM12878	blood:	n/a	chr4:54569076-54569090 chr4:54569078-54569089
4	MAZ	chr4:54568551-54569456	GM12878	blood:	n/a	n/a
5	MEF2C	chr4:54568759-54569452	GM12878	blood:	n/a	chr4:54569076-54569090 chr4:54569078-54569089 chr4:54569074-54569089
6	ZNF143	chr4:54569223-54569436	Hela-S3	cervix:	n/a	n/a
7	MEF2C	chr4:54568860-54569282	GM12878	blood:	n/a	chr4:54569076-54569090 chr4:54569078-54569089 chr4:54569074-54569089
8	MAX	chr4:54568653-54569397	ECC-1	luminal epithelium:	n/a	chr4:54569168-54569178
9	BCLAF1	chr4:54568668-54569520	GM12878	blood:	n/a	chr4:54569093-54569102 chr4:54568729-54568742
10	POLR2A	chr4:54568449-54569563	GM12878	blood:	n/a	n/a
11	TCF12	chr4:54568434-54569979	SK-N-SH	brain:	n/a	n/a
12	PAX5	chr4:54568582-54569575	GM12878	blood:	n/a	n/a
13	POLR2A	chr4:54568268-54569546	GM19099	blood:	n/a	n/a
14	SP1	chr4:54568666-54569236	A549	lung:	n/a	chr4:54568962-54568974 chr4:54568963-54568973 chr4:54568963-54568972
15	POLR2A	chr4:54569082-54569416	GM12878	blood:	n/a	n/a
16	FOXM1	chr4:54568750-54569487	GM12878	blood:	n/a	n/a
17	CREB1	chr4:54569115-54569437	A549	lung:	n/a	n/a
18	CUX1	chr4:54568375-54569502	GM12878	blood:	n/a	n/a
19	TBP	chr4:54568892-54569423	Hela-S3	cervix:	n/a	chr4:54568904-54568915
20	TCF12	chr4:54568786-54569384	GM12878	blood:	n/a	n/a
21	EP300	chr4:54568871-54569316	GM12878	blood:	n/a	chr4:54569007-54569017
22	POLR2A	chr4:54568616-54569591	HUVEC	blood vessel:	n/a	n/a
23	ELF1	chr4:54568676-54569327	GM12878	blood:	n/a	n/a
24	STAT5A	chr4:54568925-54569488	GM12878	blood:	n/a	chr4:54569330-54569338
25	BRCA1	chr4:54568745-54569423	GM12878	blood:	n/a	n/a
26	RFX5	chr4:54568532-54569261	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr4:54568503-54569610	U87	brain:	n/a	n/a
28	RELA	chr4:54568492-54569428	GM19193	blood:	n/a	n/a
29	MTA3	chr4:54568463-54569634	GM12878	blood:	n/a	n/a
30	NFIC	chr4:54568476-54569496	GM12878	blood:	n/a	chr4:54569290-54569307 chr4:54569291-54569307
31	RELA	chr4:54568515-54569491	GM10847	blood:	n/a	n/a
32	PML	chr4:54568397-54569471	GM12878	blood:	n/a	n/a
33	YY1	chr4:54568498-54569709	SK-N-SH_RA	brain:	n/a	chr4:54568734-54568745
34	CTCF	chr4:54568431-54569403	GM12878	blood:	n/a	n/a
35	KAP1	chr4:54568463-54569568	U2OS	brain:	n/a	n/a
36	BRCA1	chr4:54568706-54569407	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr4:54568317-54569510	GM18505	blood:	n/a	n/a
38	STAT3	chr4:54568945-54569583	GM12878	blood:	n/a	chr4:54569330-54569338
39	NFIC	chr4:54568607-54569652	ECC-1	luminal epithelium:	n/a	chr4:54569290-54569307 chr4:54569291-54569307
40	REST	chr4:54568763-54569263	PFSK-1	brain:	n/a	n/a
41	NFIC	chr4:54568565-54569622	SK-N-SH	brain:	n/a	chr4:54569290-54569307 chr4:54569291-54569307
42	MAX	chr4:54568678-54569448	ECC-1	luminal epithelium:	n/a	chr4:54569168-54569178
43	REST	chr4:54569089-54569501	SK-N-SH	brain:	n/a	n/a
44	RELA	chr4:54568573-54569585	GM18505	blood:	n/a	n/a
45	NR3C1	chr4:54569186-54569445	A549	lung:	n/a	n/a
46	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
47	RELA	chr4:54568542-54569633	GM12891	blood:	n/a	n/a
48	FOXA2	chr4:54568579-54569399	A549	lung:	n/a	n/a
49	E2F6	chr4:54568799-54569434	H1-hESC	embryonic stem cell:	n/a	n/a
50	KAP1	chr4:54568533-54569662	HEK293	kidney:	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: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs17083362	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3762880	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3915416	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56982325	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57066736	0.82[AMR][1000 genomes]
rs6554124	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs714146	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73817047	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73817048	0.82[ASN][1000 genomes]
rs7686371	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7699271	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7699804	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

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	chr4:54568400-54569400	Active TSS	Brain Hippocampus Middle	brain
4	chr4:54568400-54569600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:54568400-54569600	Flanking Active TSS	Liver	Liver
6	chr4:54568400-54569600	Enhancers	Fetal Brain Male	brain
7	chr4:54568400-54569800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:54568400-54569800	Flanking Active TSS	Hela-S3	cervix
9	chr4:54568600-54569400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:54568600-54569400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr4:54568600-54569400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr4:54568600-54569400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr4:54568600-54569400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr4:54568600-54569400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:54568600-54569400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:54568600-54569400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr4:54568600-54569400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr4:54568600-54569400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:54568600-54569400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
20	chr4:54568600-54569400	Active TSS	Colon Smooth Muscle	Colon
21	chr4:54568600-54569400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr4:54568600-54569400	Active TSS	Fetal Brain Female	brain
23	chr4:54568600-54569400	Active TSS	Fetal Kidney	kidney
24	chr4:54568600-54569400	Flanking Active TSS	Fetal Muscle Leg	muscle
25	chr4:54568600-54569400	Flanking Active TSS	Pancreas	Pancrea
26	chr4:54568600-54569400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr4:54568600-54569400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr4:54568600-54569400	Flanking Active TSS	HSMMtube	muscle
29	chr4:54568600-54569600	Enhancers	H1 Cell Line	embryonic stem cell
30	chr4:54568600-54569600	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr4:54568600-54569600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:54568600-54569600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:54568600-54569600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr4:54568600-54569600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:54568600-54569600	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr4:54568600-54569600	Enhancers	Gastric	stomach
37	chr4:54568600-54569600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr4:54568600-54569600	Flanking Active TSS	Right Atrium	heart
39	chr4:54568600-54569600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr4:54568600-54569600	Enhancers	Stomach Mucosa	stomach
41	chr4:54568600-54569600	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr4:54568600-54569600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr4:54568600-54569600	Flanking Active TSS	NH-A	brain
44	chr4:54568600-54569600	Flanking Active TSS	NHDF-Ad	bronchial
45	chr4:54568600-54569600	Flanking Active TSS	NHLF	lung
46	chr4:54568600-54569800	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr4:54568600-54569800	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr4:54568600-54569800	Enhancers	Placenta	Placenta
49	chr4:54568600-54569800	Enhancers	Fetal Thymus	thymus
50	chr4:54568600-54569800	Enhancers	Lung	lung

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