Variant report

Variant	rs73155678
Chromosome Location	chr4:56411777-56411778
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	POLR2A	chr4:56411760-56413743	GM12892	blood:	n/a	n/a
2	PML	chr4:56411494-56412602	GM12878	blood:	n/a	chr4:56412040-56412048
3	TCF7L2	chr4:56411457-56411986	MCF-7	breast:	n/a	n/a
4	GABPA	chr4:56411776-56412432	SK-N-SH	brain:	n/a	n/a
5	STAT3	chr4:56411693-56412251	GM12878	blood:	n/a	n/a
6	TAF1	chr4:56411772-56412519	SK-N-SH	brain:	n/a	n/a
7	TRIM28	chr4:56411684-56412345	K562	blood:	n/a	chr4:56412040-56412048
8	CEBPB	chr4:56411274-56411928	K562	blood:	n/a	chr4:56411555-56411566 chr4:56411555-56411564 chr4:56411555-56411564 chr4:56411555-56411566 chr4:56411553-56411566 chr4:56411553-56411566 chr4:56411553-56411564 chr4:56411553-56411566 chr4:56411555-56411564 chr4:56411555-56411564
9	GATA2	chr4:56411769-56412248	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr4:56411411-56413548	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr4:56411691-56412490	HUVEC	blood vessel:	n/a	n/a
12	EP300	chr4:56411688-56413646	SK-N-SH	brain:	n/a	chr4:56412374-56412390 chr4:56412075-56412091
13	IRF1	chr4:56411673-56412251	K562	blood:	n/a	chr4:56412037-56412051 chr4:56412035-56412049 chr4:56412038-56412049
14	POLR2A	chr4:56411764-56412641	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr4:56411697-56413694	K562	blood:	n/a	n/a
16	RELA	chr4:56411723-56412461	GM15510	blood:	n/a	n/a
17	TCF7L2	chr4:56411227-56412025	HEK293	kidney:	n/a	n/a
18	CHD2	chr4:56411727-56413487	K562	blood:	n/a	chr4:56412052-56412062
19	MTA3	chr4:56411580-56412639	GM12878	blood:	n/a	n/a
20	FOS	chr4:56411744-56411977	MCF10A-Er-Src	breast:	n/a	n/a
21	TCF7L2	chr4:56411497-56413490	HCT-116	colon:	n/a	n/a
22	FOXM1	chr4:56411382-56411881	ECC-1	luminal epithelium:	n/a	n/a
23	STAT5A	chr4:56411650-56412477	GM12878	blood:	n/a	n/a
24	TCF7L2	chr4:56411573-56412169	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr4:56411682-56413984	SK-N-MC	brain:	n/a	n/a
26	POLR2A	chr4:56411684-56412764	U87	brain:	n/a	n/a
27	MYC	chr4:56411776-56413367	K562	blood:	n/a	n/a
28	GABPA	chr4:56411776-56412327	K562	blood:	n/a	n/a
29	RAD21	chr4:56411502-56412283	IMR90	lung:	n/a	n/a
30	TEAD4	chr4:56411216-56412438	K562	blood:	n/a	n/a
31	POLR2A	chr4:56411742-56413454	K562	blood:	n/a	n/a
32	POLR2A	chr4:56411765-56412429	GM12878	blood:	n/a	n/a
33	CEBPD	chr4:56411406-56412330	K562	blood:	n/a	chr4:56411555-56411564
34	TAF1	chr4:56411741-56413434	K562	blood:	n/a	n/a
35	MAZ	chr4:56411530-56414133	IMR90	lung:	n/a	n/a
36	EP300	chr4:56411711-56412369	K562	blood:	n/a	chr4:56412075-56412091
37	EP300	chr4:56411354-56411791	GM12878	blood:	n/a	chr4:56411554-56411568
38	POLR2A	chr4:56411287-56413878	K562	blood:	n/a	n/a
39	FOXM1	chr4:56411732-56412402	GM12878	blood:	n/a	n/a
40	POLR2A	chr4:56411753-56412592	GM12892	blood:	n/a	n/a
41	POLR2A	chr4:56411263-56413988	GM12891	blood:	n/a	n/a
42	CEBPB	chr4:56411374-56411788	ECC-1	luminal epithelium:	n/a	chr4:56411555-56411566 chr4:56411555-56411564 chr4:56411555-56411564 chr4:56411555-56411566 chr4:56411553-56411566 chr4:56411553-56411566 chr4:56411553-56411564 chr4:56411553-56411566 chr4:56411555-56411564 chr4:56411555-56411564
43	POLR2A	chr4:56411720-56412578	GM12892	blood:	n/a	n/a
44	POLR2A	chr4:56411764-56412563	GM12878	blood:	n/a	n/a
45	POLR2A	chr4:56411744-56413323	HL-60	blood:	n/a	n/a
46	POLR2A	chr4:56411759-56413859	GM12878	blood:	n/a	n/a
47	MXI1	chr4:56411663-56414396	IMR90	lung:	n/a	n/a
48	CEBPB	chr4:56411338-56411806	ECC-1	luminal epithelium:	n/a	chr4:56411555-56411566 chr4:56411555-56411564 chr4:56411555-56411564 chr4:56411555-56411566 chr4:56411553-56411566 chr4:56411553-56411566 chr4:56411553-56411564 chr4:56411553-56411566 chr4:56411555-56411564 chr4:56411555-56411564
49	GABPA	chr4:56411668-56412494	HL-60	blood:	n/a	n/a
50	POLR2A	chr4:56411665-56412533	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56403772..56408020-chr4:56410640..56413640,7	MCF-7	breast:
2	chr4:56410839..56413778-chr4:56501227..56505067,4	K562	blood:
3	chr4:56343066..56345734-chr4:56411419..56413594,3	MCF-7	breast:
4	chr4:56260988..56264413-chr4:56410743..56414640,3	K562	blood:
5	chr4:56407970..56411777-chr4:56498734..56501001,3	K562	blood:
6	chr4:56411581..56413941-chr4:57300856..57302618,2	K562	blood:
7	chr4:56411599..56413538-chr4:56502547..56504625,2	MCF-7	breast:
8	chr4:56408119..56414507-chr4:56501105..56505595,8	K562	blood:

Variant related genes	Relation type
ENSG00000272969	TF binding region
RN7SKP30	TF binding region
ENSG00000128059	Chromatin interaction
ENSG00000223305	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000249700	Chromatin interaction
ENSG00000134852	Chromatin interaction
ENSG00000109255	Chromatin interaction
ENSG00000134851	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs17086003	1.00[AMR][1000 genomes]
rs58940536	1.00[AMR][1000 genomes]
rs59669272	1.00[AMR][1000 genomes]
rs60542719	1.00[AMR][1000 genomes]
rs60853762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61510143	1.00[AMR][1000 genomes]
rs73148756	1.00[AMR][1000 genomes]
rs73148758	1.00[AMR][1000 genomes]
rs73148767	1.00[AMR][1000 genomes]
rs73149883	1.00[AMR][1000 genomes]
rs73150945	1.00[AMR][1000 genomes]
rs73150972	1.00[AMR][1000 genomes]
rs73151884	1.00[AFR][1000 genomes]
rs73152832	1.00[AMR][1000 genomes]
rs73153608	1.00[AMR][1000 genomes]
rs73153636	1.00[AMR][1000 genomes]
rs73153653	1.00[AMR][1000 genomes]
rs73153691	1.00[AMR][1000 genomes]
rs73155667	1.00[AMR][1000 genomes]
rs73155685	1.00[AMR][1000 genomes]
rs73155690	1.00[AMR][1000 genomes]
rs73155699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv3433892	chr4:56411745-56413843	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Enhancers 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:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56361600-56411800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:56401200-56411800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:56403800-56411800	Weak transcription	Lung	lung
4	chr4:56407000-56411800	Weak transcription	Gastric	stomach
5	chr4:56407000-56411800	Weak transcription	Spleen	Spleen
6	chr4:56410400-56413600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:56410400-56413800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:56410400-56414000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:56410600-56413600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:56410600-56413600	Active TSS	K562	blood
11	chr4:56410800-56411800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:56410800-56413600	Active TSS	Duodenum Mucosa	Duodenum
13	chr4:56410800-56413800	Active TSS	H1 Cell Line	embryonic stem cell
14	chr4:56410800-56413800	Active TSS	Fetal Intestine Large	intestine
15	chr4:56410800-56413800	Active TSS	Hela-S3	cervix
16	chr4:56410800-56414200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:56410800-56414200	Active TSS	NHLF	lung
18	chr4:56411000-56411800	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr4:56411000-56411800	Flanking Active TSS	Dnd41	blood
20	chr4:56411000-56413600	Active TSS	HMEC	breast
21	chr4:56411000-56413600	Active TSS	NHEK	skin
22	chr4:56411000-56413800	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr4:56411000-56413800	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr4:56411000-56413800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:56411000-56413800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:56411000-56413800	Active TSS	GM12878-XiMat	blood
27	chr4:56411000-56413800	Active TSS	NH-A	brain
28	chr4:56411000-56414000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:56411000-56414000	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr4:56411000-56414000	Active TSS	A549	lung
31	chr4:56411000-56414200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:56411000-56414200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:56411000-56414200	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr4:56411000-56414400	Active TSS	Fetal Brain Female	brain
35	chr4:56411200-56412000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:56411200-56412200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr4:56411200-56412400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr4:56411200-56412600	Active TSS	Right Atrium	heart
39	chr4:56411200-56413400	Active TSS	Colonic Mucosa	Colon
40	chr4:56411200-56413600	Active TSS	Fetal Intestine Small	intestine
41	chr4:56411200-56413600	Active TSS	Pancreas	Pancrea
42	chr4:56411200-56413800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:56411200-56413800	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr4:56411200-56413800	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr4:56411200-56413800	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr4:56411200-56413800	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr4:56411200-56413800	Active TSS	Muscle Satellite Cultured Cells	--
48	chr4:56411200-56413800	Active TSS	Fetal Kidney	kidney
49	chr4:56411200-56413800	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr4:56411200-56413800	Active TSS	Rectal Smooth Muscle	rectum

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