Variant report

Variant	rs73819635
Chromosome Location	chr4:56411523-56411524
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	PML	chr4:56411494-56412602	GM12878	blood:	n/a	chr4:56412040-56412048
2	TCF7L2	chr4:56411457-56411986	MCF-7	breast:	n/a	n/a
3	JUND	chr4:56411452-56411560	H1-hESC	embryonic stem cell:	n/a	n/a
4	NFYA	chr4:56411357-56411628	Hela-S3	cervix:	n/a	chr4:56411446-56411456 chr4:56411444-56411462
5	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
6	NFYB	chr4:56411261-56411661	GM12878	blood:	n/a	chr4:56411441-56411456 chr4:56411446-56411456
7	POLR2A	chr4:56411411-56413548	MCF10A-Er-Src	breast:	n/a	n/a
8	CEBPB	chr4:56411377-56411692	A549	lung:	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	TCF7L2	chr4:56411227-56412025	HEK293	kidney:	n/a	n/a
10	RFX5	chr4:56411314-56411689	K562	blood:	n/a	chr4:56411447-56411456
11	TCF7L2	chr4:56411497-56413490	HCT-116	colon:	n/a	n/a
12	FOXM1	chr4:56411382-56411881	ECC-1	luminal epithelium:	n/a	n/a
13	RAD21	chr4:56411502-56412283	IMR90	lung:	n/a	n/a
14	TEAD4	chr4:56411216-56412438	K562	blood:	n/a	n/a
15	GATA3	chr4:56411489-56411717	SH-SY5Y	brain:	n/a	n/a
16	CEBPD	chr4:56411406-56412330	K562	blood:	n/a	chr4:56411555-56411564
17	CEBPB	chr4:56411383-56411734	A549	lung:	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
18	EP300	chr4:56411354-56411791	GM12878	blood:	n/a	chr4:56411554-56411568
19	POLR2A	chr4:56411287-56413878	K562	blood:	n/a	n/a
20	POLR2A	chr4:56411263-56413988	GM12891	blood:	n/a	n/a
21	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
22	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
23	CEBPB	chr4:56411371-56411663	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
24	BRCA1	chr4:56411438-56412308	Hela-S3	cervix:	n/a	n/a
25	CEBPB	chr4:56411379-56411719	MCF-7	breast:	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
26	TBP	chr4:56410958-56412334	Hela-S3	cervix:	n/a	n/a
27	CEBPB	chr4:56411375-56411925	IMR90	lung:	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
28	CHD1	chr4:56411491-56412415	GM12878	blood:	n/a	chr4:56412052-56412062
29	UBTF	chr4:56411497-56412563	K562	blood:	n/a	n/a
30	TBP	chr4:56411397-56412310	GM12878	blood:	n/a	n/a
31	RCOR1	chr4:56411412-56412459	Hela-S3	cervix:	n/a	n/a
32	CEBPB	chr4:56411377-56411750	H1-hESC	embryonic stem cell:	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
33	CEBPB	chr4:56411358-56411749	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
34	ARID3A	chr4:56411458-56412170	K562	blood:	n/a	n/a
35	MXI1	chr4:56410957-56414953	SK-N-SH	brain:	n/a	n/a
36	RCOR1	chr4:56411364-56414002	K562	blood:	n/a	n/a
37	IRF1	chr4:56411464-56412305	K562	blood:	n/a	chr4:56412037-56412051 chr4:56412035-56412049 chr4:56411478-56411485 chr4:56412038-56412049
38	CEBPB	chr4:56411355-56411859	MCF-7	breast:	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
39	RFX5	chr4:56411235-56412581	Hela-S3	cervix:	n/a	chr4:56412113-56412127 chr4:56411447-56411456
40	HCFC1	chr4:56411259-56413698	Hela-S3	cervix:	n/a	n/a
41	CEBPB	chr4:56411279-56411835	A549	lung:	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
42	CUX1	chr4:56411491-56412176	GM12878	blood:	n/a	n/a
43	CEBPB	chr4:56411008-56412385	Hela-S3	cervix:	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
44	POLR2A	chr4:56411274-56411581	HCT-116	colon:	n/a	n/a
45	NFYB	chr4:56411349-56411627	Hela-S3	cervix:	n/a	chr4:56411441-56411456 chr4:56411446-56411456
46	FOS	chr4:56411425-56411572	MCF10A-Er-Src	breast:	n/a	chr4:56411448-56411457
47	MYC	chr4:56410958-56412348	MCF10A-Er-Src	breast:	n/a	n/a
48	TCF7L2	chr4:56411368-56412313	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr4:56410987-56413569	MCF10A-Er-Src	breast:	n/a	n/a
50	ARID3A	chr4:56411386-56412352	HepG2	liver:	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	chr4:56408119..56414507-chr4:56501105..56505595,8	K562	blood:

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

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10031586	1.00[EUR][1000 genomes]
rs1488940	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1533803	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1554482	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17085739	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17085769	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17085780	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17085821	1.00[EUR][1000 genomes]
rs2130039	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2140076	1.00[EUR][1000 genomes]
rs2412660	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35150421	1.00[EUR][1000 genomes]
rs57219525	1.00[EUR][1000 genomes]
rs57848550	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58395965	1.00[EUR][1000 genomes]
rs6820823	1.00[EUR][1000 genomes]
rs6847415	1.00[EUR][1000 genomes]
rs6855837	1.00[EUR][1000 genomes]
rs73149762	1.00[EUR][1000 genomes]
rs73151873	1.00[EUR][1000 genomes]
rs73151889	1.00[EUR][1000 genomes]
rs73153687	1.00[EUR][1000 genomes]
rs73817206	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73819624	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73819626	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73819631	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73819633	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73819636	0.88[AFR][1000 genomes]
rs73819642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73819647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7655255	1.00[EUR][1000 genomes]
rs7693751	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:120 , 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	chr4:56396800-56411600	Weak transcription	Psoas Muscle	Psoas
3	chr4:56399600-56411600	Weak transcription	Left Ventricle	heart
4	chr4:56401200-56411800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:56402800-56411600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:56403800-56411800	Weak transcription	Lung	lung
7	chr4:56407000-56411600	Weak transcription	Aorta	Aorta
8	chr4:56407000-56411800	Weak transcription	Gastric	stomach
9	chr4:56407000-56411800	Weak transcription	Spleen	Spleen
10	chr4:56410000-56411600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr4:56410200-56411600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:56410400-56411600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:56410400-56413600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:56410400-56413800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:56410400-56414000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:56410600-56413600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:56410600-56413600	Active TSS	K562	blood
18	chr4:56410800-56411600	Flanking Active TSS	Osteobl	bone
19	chr4:56410800-56411800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:56410800-56413600	Active TSS	Duodenum Mucosa	Duodenum
21	chr4:56410800-56413800	Active TSS	H1 Cell Line	embryonic stem cell
22	chr4:56410800-56413800	Active TSS	Fetal Intestine Large	intestine
23	chr4:56410800-56413800	Active TSS	Hela-S3	cervix
24	chr4:56410800-56414200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:56410800-56414200	Active TSS	NHLF	lung
26	chr4:56411000-56411600	Flanking Active TSS	Fetal Lung	lung
27	chr4:56411000-56411600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr4:56411000-56411600	Active TSS	HepG2	liver
29	chr4:56411000-56411600	Flanking Active TSS	HUVEC	blood vessel
30	chr4:56411000-56411800	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr4:56411000-56411800	Flanking Active TSS	Dnd41	blood
32	chr4:56411000-56413600	Active TSS	HMEC	breast
33	chr4:56411000-56413600	Active TSS	NHEK	skin
34	chr4:56411000-56413800	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr4:56411000-56413800	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr4:56411000-56413800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:56411000-56413800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:56411000-56413800	Active TSS	GM12878-XiMat	blood
39	chr4:56411000-56413800	Active TSS	NH-A	brain
40	chr4:56411000-56414000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:56411000-56414000	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr4:56411000-56414000	Active TSS	A549	lung
43	chr4:56411000-56414200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:56411000-56414200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:56411000-56414200	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr4:56411000-56414400	Active TSS	Fetal Brain Female	brain
47	chr4:56411200-56411600	Enhancers	Primary T cells fromperipheralblood	blood
48	chr4:56411200-56411600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:56411200-56411600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr4:56411200-56411600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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