Variant report

Variant	rs73153344
Chromosome Location	chr4:54568780-54568781
allele	A/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	MAZ	chr4:54568551-54569456	GM12878	blood:	n/a	n/a
2	MEF2C	chr4:54568759-54569452	GM12878	blood:	n/a	chr4:54569076-54569090 chr4:54569078-54569089 chr4:54569074-54569089
3	ZNF143	chr4:54568570-54568981	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr4:54568780-54568930	RPTEC	kidney:	n/a	n/a
5	MAX	chr4:54568653-54569397	ECC-1	luminal epithelium:	n/a	chr4:54569168-54569178
6	RAD21	chr4:54568491-54568897	H1-hESC	embryonic stem cell:	n/a	n/a
7	BCLAF1	chr4:54568668-54569520	GM12878	blood:	n/a	chr4:54569093-54569102 chr4:54568729-54568742
8	POLR2A	chr4:54568449-54569563	GM12878	blood:	n/a	n/a
9	TCF12	chr4:54568434-54569979	SK-N-SH	brain:	n/a	n/a
10	PAX5	chr4:54568582-54569575	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:54568661-54569067	IMR90	lung:	n/a	n/a
12	POLR2A	chr4:54568268-54569546	GM19099	blood:	n/a	n/a
13	SP1	chr4:54568666-54569236	A549	lung:	n/a	chr4:54568962-54568974 chr4:54568963-54568973 chr4:54568963-54568972
14	FOXM1	chr4:54568750-54569487	GM12878	blood:	n/a	n/a
15	CUX1	chr4:54568375-54569502	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:54568616-54569591	HUVEC	blood vessel:	n/a	n/a
17	ELF1	chr4:54568676-54569327	GM12878	blood:	n/a	n/a
18	BRCA1	chr4:54568745-54569423	GM12878	blood:	n/a	n/a
19	RFX5	chr4:54568532-54569261	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr4:54568503-54569610	U87	brain:	n/a	n/a
21	RELA	chr4:54568492-54569428	GM19193	blood:	n/a	n/a
22	MTA3	chr4:54568463-54569634	GM12878	blood:	n/a	n/a
23	NFIC	chr4:54568476-54569496	GM12878	blood:	n/a	chr4:54569290-54569307 chr4:54569291-54569307
24	RELA	chr4:54568515-54569491	GM10847	blood:	n/a	n/a
25	PML	chr4:54568397-54569471	GM12878	blood:	n/a	n/a
26	YY1	chr4:54568498-54569709	SK-N-SH_RA	brain:	n/a	chr4:54568734-54568745
27	CTCF	chr4:54568431-54569403	GM12878	blood:	n/a	n/a
28	KAP1	chr4:54568463-54569568	U2OS	brain:	n/a	n/a
29	BRCA1	chr4:54568706-54569407	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr4:54568317-54569510	GM18505	blood:	n/a	n/a
31	CTCF	chr4:54568780-54568930	HVMF	connective:	n/a	n/a
32	NFIC	chr4:54568607-54569652	ECC-1	luminal epithelium:	n/a	chr4:54569290-54569307 chr4:54569291-54569307
33	REST	chr4:54568763-54569263	PFSK-1	brain:	n/a	n/a
34	NFIC	chr4:54568565-54569622	SK-N-SH	brain:	n/a	chr4:54569290-54569307 chr4:54569291-54569307
35	MAX	chr4:54568678-54569448	ECC-1	luminal epithelium:	n/a	chr4:54569168-54569178
36	RELA	chr4:54568573-54569585	GM18505	blood:	n/a	n/a
37	HMGN3	chr4:54568693-54568999	K562	blood:	n/a	n/a
38	POLR2A	chr4:54568565-54569028	GM12878	blood:	n/a	n/a
39	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
40	RELA	chr4:54568542-54569633	GM12891	blood:	n/a	n/a
41	FOXA2	chr4:54568579-54569399	A549	lung:	n/a	n/a
42	KAP1	chr4:54568533-54569662	HEK293	kidney:	n/a	n/a
43	E2F6	chr4:54568708-54569434	A549	lung:	n/a	n/a
44	EP300	chr4:54568521-54569679	SK-N-SH	brain:	n/a	chr4:54568734-54568750 chr4:54569007-54569017
45	POLR2A	chr4:54568537-54569490	GM19193	blood:	n/a	n/a
46	EP300	chr4:54568677-54569784	SK-N-SH_RA	brain:	n/a	chr4:54568734-54568750 chr4:54569007-54569017
47	SP1	chr4:54568516-54569521	GM12878	blood:	n/a	chr4:54568641-54568648 chr4:54568962-54568974 chr4:54569331-54569345 chr4:54568963-54568973 chr4:54568963-54568972
48	EP300	chr4:54568459-54569770	SK-N-SH_RA	brain:	n/a	chr4:54568734-54568750 chr4:54569007-54569017
49	POLR2A	chr4:54568544-54569478	GM12892	blood:	n/a	n/a
50	MAX	chr4:54568695-54569439	A549	lung:	n/a	chr4:54569168-54569178

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54486968..54487480-chr4:54567881..54568820,2	MCF-7	breast:
2	chr4:54568125..54570977-chr4:54571339..54573651,2	K562	blood:

Variant related genes	Relation type
LNX1	TF binding region

rs_ID	r²[population]
rs13434889	1.00[AMR][1000 genomes]
rs17082954	1.00[AMR][1000 genomes]
rs28470966	1.00[AMR][1000 genomes]
rs28564139	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28605676	1.00[AMR][1000 genomes]
rs28702938	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3762881	1.00[AMR][1000 genomes]
rs73817121	1.00[AMR][1000 genomes]
rs73817123	1.00[AMR][1000 genomes]
rs73817127	1.00[AMR][1000 genomes]
rs73817134	1.00[AMR][1000 genomes]
rs9994943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54566400-54568800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:54568000-54569000	Enhancers	Fetal Lung	lung
3	chr4:54568000-54569600	Flanking Active TSS	GM12878-XiMat	blood
4	chr4:54568000-54569800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr4:54568200-54568800	Enhancers	Primary B cells from cord blood	blood
6	chr4:54568200-54568800	Enhancers	Fetal Heart	heart
7	chr4:54568400-54568800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:54568400-54568800	Flanking Active TSS	Brain Substantia Nigra	brain
9	chr4:54568400-54569000	Enhancers	HMEC	breast
10	chr4:54568400-54569200	Active TSS	HepG2	liver
11	chr4:54568400-54569400	Active TSS	Brain Hippocampus Middle	brain
12	chr4:54568400-54569600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:54568400-54569600	Flanking Active TSS	Liver	Liver
14	chr4:54568400-54569600	Enhancers	Fetal Brain Male	brain
15	chr4:54568400-54569800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:54568400-54569800	Flanking Active TSS	Hela-S3	cervix
17	chr4:54568600-54568800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:54568600-54568800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:54568600-54568800	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr4:54568600-54568800	Flanking Active TSS	Colonic Mucosa	Colon
21	chr4:54568600-54568800	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr4:54568600-54568800	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr4:54568600-54568800	Active TSS	Fetal Intestine Large	intestine
24	chr4:54568600-54568800	Flanking Active TSS	Ovary	ovary
25	chr4:54568600-54568800	Active TSS	HSMM	muscle
26	chr4:54568600-54569000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr4:54568600-54569000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:54568600-54569000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:54568600-54569000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:54568600-54569000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:54568600-54569000	Enhancers	Aorta	Aorta
32	chr4:54568600-54569000	Active TSS	Brain Germinal Matrix	brain
33	chr4:54568600-54569000	Flanking Active TSS	Esophagus	oesophagus
34	chr4:54568600-54569000	Flanking Active TSS	Right Ventricle	heart
35	chr4:54568600-54569000	Active TSS	Thymus	Thymus
36	chr4:54568600-54569000	Active TSS	A549	lung
37	chr4:54568600-54569200	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr4:54568600-54569200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:54568600-54569200	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr4:54568600-54569200	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr4:54568600-54569200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:54568600-54569200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:54568600-54569200	Active TSS	Brain Angular Gyrus	brain
44	chr4:54568600-54569200	Active TSS	Brain Anterior Caudate	brain
45	chr4:54568600-54569200	Flanking Active TSS	Fetal Intestine Small	intestine
46	chr4:54568600-54569200	Flanking Active TSS	Fetal Muscle Trunk	muscle
47	chr4:54568600-54569200	Active TSS	Left Ventricle	heart
48	chr4:54568600-54569200	Active TSS	Psoas Muscle	Psoas
49	chr4:54568600-54569200	Active TSS	Rectal Smooth Muscle	rectum
50	chr4:54568600-54569200	Flanking Active TSS	NHEK	skin

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