Variant report

Variant	rs4145516
Chromosome Location	chr4:190862511-190862512
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	TFAP2C	chr4:190861230-190862627	Hela-S3	cervix:	n/a	n/a
2	POU2F2	chr4:190859811-190862598	GM12878	blood:	n/a	n/a
3	MTA3	chr4:190861173-190862634	GM12878	blood:	n/a	n/a
4	CHD1	chr4:190861225-190862591	GM12878	blood:	n/a	chr4:190861668-190861678 chr4:190862084-190862094
5	POU2F2	chr4:190860778-190862561	GM12891	blood:	n/a	n/a
6	EGR1	chr4:190861360-190862646	HCT-116	colon:	n/a	chr4:190862277-190862290 chr4:190862276-190862290 chr4:190862278-190862287 chr4:190862278-190862289 chr4:190862272-190862294 chr4:190862367-190862377 chr4:190862277-190862290 chr4:190861978-190861987 chr4:190862276-190862291 chr4:190862278-190862288 chr4:190862277-190862290
7	EGR1	chr4:190861363-190862570	HCT-116	colon:	n/a	chr4:190862277-190862290 chr4:190862276-190862290 chr4:190862278-190862287 chr4:190862278-190862289 chr4:190862272-190862294 chr4:190862367-190862377 chr4:190862277-190862290 chr4:190861978-190861987 chr4:190862276-190862291 chr4:190862278-190862288 chr4:190862277-190862290
8	UBTF	chr4:190860737-190862933	K562	blood:	n/a	n/a
9	NR2F2	chr4:190861785-190862544	K562	blood:	n/a	n/a
10	POLR2A	chr4:190861196-190862512	A549	lung:	n/a	n/a
11	RELA	chr4:190860850-190862528	GM15510	blood:	n/a	n/a
12	ZMIZ1	chr4:190861211-190862523	K562	blood:	n/a	n/a
13	SETDB1	chr4:190861208-190862523	K562	blood:	n/a	chr4:190861225-190861249
14	HEY1	chr4:190861473-190862558	HepG2	liver:	n/a	chr4:190861719-190861734
15	TAF1	chr4:190861483-190862519	K562	blood:	n/a	n/a
16	EBF1	chr4:190862373-190862808	GM12878	blood:	n/a	chr4:190862483-190862493
17	MXI1	chr4:190861498-190862547	HepG2	liver:	n/a	n/a
18	POLR2A	chr4:190860914-190862524	K562	blood:	n/a	n/a
19	HMGN3	chr4:190861218-190862535	K562	blood:	n/a	n/a
20	TAF1	chr4:190861125-190862593	H1-hESC	embryonic stem cell:	n/a	n/a
21	JUN	chr4:190861488-190862531	K562	blood:	n/a	n/a
22	POLR2A	chr4:190859787-190862570	GM12892	blood:	n/a	n/a
23	RUNX3	chr4:190861334-190862549	GM12878	blood:	n/a	n/a
24	TCF12	chr4:190861503-190862578	ECC-1	luminal epithelium:	n/a	n/a
25	MAX	chr4:190861148-190862597	ECC-1	luminal epithelium:	n/a	n/a
26	HEY1	chr4:190860708-190862632	K562	blood:	n/a	chr4:190861719-190861734
27	POLR2A	chr4:190861305-190862529	K562	blood:	n/a	n/a
28	POLR2A	chr4:190860898-190862516	GM12878	blood:	n/a	n/a
29	POLR2A	chr4:190860516-190862535	H1-hESC	embryonic stem cell:	n/a	n/a
30	NR2C2	chr4:190861394-190862558	Hela-S3	cervix:	n/a	chr4:190862453-190862466
31	EGR1	chr4:190861488-190862529	ECC-1	luminal epithelium:	n/a	chr4:190862277-190862290 chr4:190862276-190862290 chr4:190862278-190862287 chr4:190862278-190862289 chr4:190862272-190862294 chr4:190862367-190862377 chr4:190862277-190862290 chr4:190861978-190861987 chr4:190862276-190862291 chr4:190862278-190862288 chr4:190862277-190862290
32	PAX5	chr4:190862395-190862549	GM12878	blood:	n/a	n/a
33	TRIM28	chr4:190860991-190862512	K562	blood:	n/a	n/a
34	POLR2A	chr4:190861308-190862633	PBDE	blood:	n/a	n/a
35	POLR2A	chr4:190861161-190862594	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr4:190861470-190862516	MCF10A-Er-Src	breast:	n/a	n/a
37	CTCF	chr4:190861127-190862527	SK-N-SH	brain:	n/a	n/a
38	YY1	chr4:190861334-190862537	HepG2	liver:	n/a	chr4:190861599-190861621 chr4:190861735-190861749 chr4:190861706-190861720 chr4:190861720-190861729 chr4:190861610-190861618
39	CUX1	chr4:190860658-190863087	K562	blood:	n/a	chr4:190862564-190862578
40	POLR2A	chr4:190861099-190862532	K562	blood:	n/a	n/a
41	MAX	chr4:190861140-190862537	A549	lung:	n/a	n/a
42	CTCF	chr4:190861144-190862549	A549	lung:	n/a	n/a
43	NR2F2	chr4:190861158-190862690	K562	blood:	n/a	n/a
44	YY1	chr4:190861199-190862541	SK-N-SH_RA	brain:	n/a	chr4:190861599-190861621 chr4:190861735-190861749 chr4:190861706-190861720 chr4:190861720-190861729 chr4:190861610-190861618
45	POLR2A	chr4:190860076-190862637	GM12892	blood:	n/a	n/a
46	EBF1	chr4:190862227-190862570	GM12878	blood:	n/a	chr4:190862483-190862493
47	SMARCB1	chr4:190861210-190862557	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr4:190861163-190862573	K562	blood:	n/a	n/a
49	POLR2A	chr4:190860758-190862572	GM12891	blood:	n/a	n/a
50	POLR2A	chr4:190861506-190862517	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:190860824..190863306-chr5:162931181..162932933,2	MCF-7	breast:
2	chr20:29611333..29612723-chr4:190861521..190862825,5	HCT-116	colon:
3	chr20:29610673..29612888-chr4:190860203..190862511,3	MCF-7	breast:
4	chr20:29611333..29614057-chr4:190860675..190863034,4	MCF-7	breast:
5	chr20:29609593..29613129-chr4:190859723..190863221,5	K562	blood:
6	chr20:29611128..29612321-chr4:190861463..190862739,6	MCF-7	breast:
7	chr20:29611632..29612497-chr4:190861809..190862721,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245685	TF binding region
ENSG00000149531	Chromatin interaction
ENSG00000038274	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10001956	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11132770	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11132771	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11736387	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12646565	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12646667	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12649488	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13121836	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13121986	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13133725	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13133958	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13148101	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1961818	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2037947	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2037948	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2078634	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2411549	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4145515	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4145517	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6553396	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6816856	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6820684	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6837422	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7657916	0.86[EUR][1000 genomes]
rs7658339	0.85[EUR][1000 genomes]
rs7668489	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7691161	0.82[EUR][1000 genomes]
rs9992042	0.82[EUR][1000 genomes]
rs9996679	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4145516	AF146191.4	cis	Esophagus Muscularis	GTEx
rs4145516	AF146191.4	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:190858600-190865400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
2	chr4:190860600-190864200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
3	chr4:190860800-190862600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:190860800-190862600	ZNF genes & repeats	Dnd41	blood
5	chr4:190860800-190862800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:190860800-190862800	Active TSS	Colon Smooth Muscle	Colon
7	chr4:190860800-190862800	Active TSS	Fetal Heart	heart
8	chr4:190860800-190863800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
9	chr4:190860800-190863800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr4:190860800-190863800	ZNF genes & repeats	Fetal Brain Male	brain
11	chr4:190860800-190864000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
12	chr4:190861000-190862600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:190861000-190862600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr4:190861000-190862600	Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr4:190861000-190862600	ZNF genes & repeats	Esophagus	oesophagus
16	chr4:190861000-190862600	ZNF genes & repeats	Lung	lung
17	chr4:190861000-190862600	ZNF genes & repeats	Thymus	Thymus
18	chr4:190861000-190862600	ZNF genes & repeats	Spleen	Spleen
19	chr4:190861000-190863000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
20	chr4:190861000-190863200	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr4:190861000-190863200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
22	chr4:190861000-190863200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:190861000-190863200	Active TSS	A549	lung
24	chr4:190861000-190863600	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr4:190861000-190863800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:190861000-190863800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
27	chr4:190861200-190862600	ZNF genes & repeats	Fetal Intestine Large	intestine
28	chr4:190861200-190862600	Active TSS	Fetal Lung	lung
29	chr4:190861200-190862800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr4:190861200-190862800	Active TSS	Brain Angular Gyrus	brain
31	chr4:190861200-190862800	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr4:190861200-190862800	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr4:190861200-190862800	Active TSS	Stomach Smooth Muscle	stomach
34	chr4:190861200-190862800	Active TSS	Osteobl	bone
35	chr4:190861200-190863000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:190861200-190863000	Active TSS	HSMMtube	muscle
37	chr4:190861200-190863200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:190861200-190863200	Active TSS	Hela-S3	cervix
39	chr4:190861200-190863200	Active TSS	NHDF-Ad	bronchial
40	chr4:190861200-190863400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:190861200-190863400	Active TSS	Right Atrium	heart
42	chr4:190861200-190863800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:190861200-190863800	ZNF genes & repeats	HMEC	breast
44	chr4:190861400-190862800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr4:190861400-190862800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:190861400-190862800	Active TSS	Small Intestine	intestine
47	chr4:190861400-190863200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr4:190861400-190863200	Active TSS	Ovary	ovary
49	chr4:190861600-190862600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr4:190861600-190862600	Active TSS	Primary T cells from cord blood	blood

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