Variant report

Variant	rs56753131
Chromosome Location	chr4:54569665-54569666
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	TCF12	chr4:54568434-54569979	SK-N-SH	brain:	n/a	n/a
2	YY1	chr4:54568498-54569709	SK-N-SH_RA	brain:	n/a	chr4:54568734-54568745
3	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
4	EP300	chr4:54568521-54569679	SK-N-SH	brain:	n/a	chr4:54568734-54568750 chr4:54569007-54569017
5	EP300	chr4:54568677-54569784	SK-N-SH_RA	brain:	n/a	chr4:54568734-54568750 chr4:54569007-54569017
6	EP300	chr4:54568459-54569770	SK-N-SH_RA	brain:	n/a	chr4:54568734-54568750 chr4:54569007-54569017
7	RXRA	chr4:54568487-54569669	SK-N-SH	brain:	n/a	n/a
8	WRNIP1	chr4:54568524-54569680	GM12878	blood:	n/a	n/a
9	CHD2	chr4:54568550-54569724	GM12878	blood:	n/a	n/a
10	RAD21	chr4:54568492-54569723	SK-N-SH_RA	brain:	n/a	chr4:54569378-54569387
11	GATA3	chr4:54568597-54569699	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr4:54568584-54569790	SK-N-SH	brain:	n/a	n/a
13	NFIC	chr4:54568545-54569689	ECC-1	luminal epithelium:	n/a	chr4:54569290-54569307 chr4:54569291-54569307
14	TCF12	chr4:54568548-54569843	SK-N-SH	brain:	n/a	n/a
15	NFIC	chr4:54568430-54569768	SK-N-SH	brain:	n/a	chr4:54569290-54569307 chr4:54569291-54569307

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: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs17083326	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083355	0.87[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]
rs60293431	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6844085	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs728587	0.98[ASN][1000 genomes]
rs7671090	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54568000-54569800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr4:54568400-54569800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:54568400-54569800	Flanking Active TSS	Hela-S3	cervix
4	chr4:54568600-54569800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr4:54568600-54569800	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr4:54568600-54569800	Enhancers	Placenta	Placenta
7	chr4:54568600-54569800	Enhancers	Fetal Thymus	thymus
8	chr4:54568600-54569800	Enhancers	Lung	lung
9	chr4:54568600-54569800	Enhancers	Spleen	Spleen
10	chr4:54568600-54569800	Flanking Active TSS	HUVEC	blood vessel
11	chr4:54568600-54569800	Flanking Active TSS	Osteobl	bone
12	chr4:54568600-54570000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:54568600-54570200	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr4:54568600-54570400	Enhancers	Fetal Stomach	stomach
15	chr4:54568800-54569800	Enhancers	H9 Cell Line	embryonic stem cell
16	chr4:54568800-54569800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:54568800-54569800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:54568800-54569800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:54568800-54570200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:54569000-54569800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:54569000-54569800	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr4:54569000-54569800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:54569000-54569800	Enhancers	Fetal Intestine Large	intestine
24	chr4:54569000-54569800	Enhancers	Small Intestine	intestine
25	chr4:54569200-54569800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:54569200-54569800	Enhancers	Fetal Intestine Small	intestine
27	chr4:54569200-54569800	Enhancers	Fetal Muscle Trunk	muscle
28	chr4:54569200-54569800	Enhancers	Ovary	ovary
29	chr4:54569200-54570000	Enhancers	Primary hematopoietic stem cells	blood
30	chr4:54569200-54573200	Enhancers	Primary B cells from peripheral blood	blood
31	chr4:54569400-54569800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr4:54569400-54569800	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr4:54569400-54569800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:54569400-54569800	Enhancers	Brain Cingulate Gyrus	brain
35	chr4:54569400-54569800	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr4:54569400-54569800	Enhancers	HSMMtube	muscle
37	chr4:54569400-54570000	Enhancers	A549	lung
38	chr4:54569400-54570200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr4:54569400-54570200	Enhancers	Muscle Satellite Cultured Cells	--
40	chr4:54569400-54570200	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr4:54569400-54570200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:54569400-54570200	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr4:54569400-54570400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:54569400-54570400	Enhancers	Fetal Muscle Leg	muscle
45	chr4:54569400-54570600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr4:54569400-54571400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr4:54569400-54572400	Weak transcription	Psoas Muscle	Psoas
48	chr4:54569400-54572800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr4:54569400-54573200	Enhancers	Primary B cells from cord blood	blood
50	chr4:54569400-54577200	Weak transcription	Aorta	Aorta

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