Variant report

Variant	rs1545597
Chromosome Location	chr3:142721469-142721470
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	MAX	chr3:142719294-142721539	HepG2	liver:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
2	CEBPB	chr3:142721076-142721621	K562	blood:	n/a	chr3:142721260-142721271
3	MXI1	chr3:142719220-142721923	Hela-S3	cervix:	n/a	chr3:142721094-142721103
4	MAX	chr3:142719766-142721541	ECC-1	luminal epithelium:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
5	E2F4	chr3:142720833-142721518	MCF10A-Er-Src	breast:	n/a	n/a
6	MXI1	chr3:142719180-142721608	IMR90	lung:	n/a	chr3:142721094-142721103
7	MXI1	chr3:142719929-142721536	H1-hESC	embryonic stem cell:	n/a	chr3:142721094-142721103
8	MYC	chr3:142719887-142721480	K562	blood:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
9	MAX	chr3:142719674-142721739	A549	lung:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
10	PML	chr3:142719584-142721605	GM12878	blood:	n/a	chr3:142721578-142721586
11	HCFC1	chr3:142719752-142721562	K562	blood:	n/a	n/a
12	CEBPB	chr3:142720965-142721580	K562	blood:	n/a	chr3:142721260-142721271
13	POLR2A	chr3:142719169-142721475	IMR90	lung:	n/a	n/a
14	POLR2A	chr3:142719672-142721713	PBDE	blood:	n/a	n/a
15	POLR2A	chr3:142719380-142721545	GM18505	blood:	n/a	n/a
16	POLR2A	chr3:142719733-142721660	SK-N-MC	brain:	n/a	n/a
17	MAZ	chr3:142719843-142721606	IMR90	lung:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
18	MXI1	chr3:142719775-142721805	GM12878	blood:	n/a	chr3:142721094-142721103
19	POLR2A	chr3:142718343-142721495	HepG2	liver:	n/a	n/a
20	MAX	chr3:142719855-142721546	K562	blood:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
21	MAX	chr3:142719322-142721633	A549	lung:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
22	TBL1XR1	chr3:142721055-142722215	K562	blood:	n/a	n/a
23	MYC	chr3:142719788-142721730	K562	blood:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
24	CEBPB	chr3:142721084-142721610	IMR90	lung:	n/a	chr3:142721260-142721271
25	GTF2F1	chr3:142719388-142721516	Hela-S3	cervix:	n/a	n/a
26	MAX	chr3:142719436-142721473	NB4	blood:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
27	TBP	chr3:142719354-142721790	Hela-S3	cervix:	n/a	n/a
28	MAX	chr3:142719712-142721594	K562	blood:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
29	POLR2A	chr3:142718446-142722255	K562	blood:	n/a	n/a
30	POLR2A	chr3:142719310-142721602	K562	blood:	n/a	n/a
31	SIN3AK20	chr3:142719608-142721702	MCF-7	breast:	n/a	n/a
32	POLR2A	chr3:142719667-142721524	HL-60	blood:	n/a	n/a
33	POLR2A	chr3:142719794-142721547	H1-hESC	embryonic stem cell:	n/a	n/a
34	CEBPB	chr3:142721084-142721499	A549	lung:	n/a	chr3:142721260-142721271
35	MYC	chr3:142719296-142721779	K562	blood:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
36	E2F4	chr3:142721215-142721473	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:142719261-142721981	K562	blood:	n/a	n/a
38	MAX	chr3:142719858-142721484	H1-hESC	embryonic stem cell:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
39	POLR2A	chr3:142719326-142721640	H1-hESC	embryonic stem cell:	n/a	n/a
40	EP300	chr3:142720972-142721572	GM12878	blood:	n/a	chr3:142721419-142721433
41	MAX	chr3:142719803-142721485	MCF-7	breast:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
42	CEBPB	chr3:142719889-142721743	Hela-S3	cervix:	n/a	chr3:142721260-142721271
43	MXI1	chr3:142719844-142721577	HepG2	liver:	n/a	chr3:142721094-142721103
44	IRF1	chr3:142721061-142721606	K562	blood:	n/a	chr3:142721352-142721363 chr3:142721352-142721365
45	POLR2A	chr3:142719254-142721730	MCF10A-Er-Src	breast:	n/a	n/a
46	CEBPB	chr3:142720961-142721523	A549	lung:	n/a	chr3:142721260-142721271
47	CEBPB	chr3:142721190-142721509	K562	blood:	n/a	chr3:142721260-142721271
48	POLR2A	chr3:142719214-142721587	K562	blood:	n/a	n/a
49	MAX	chr3:142719355-142721545	Hela-S3	cervix:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
50	MAX	chr3:142720822-142721488	H1-hESC	embryonic stem cell:	n/a	chr3:142721094-142721103 chr3:142721422-142721431

No.	Distal block	Cell Line	Cell type
1	chr3:142296202..142300183-chr3:142719946..142722583,4	K562	blood:
2	chr3:142605846..142608751-chr3:142718093..142722238,5	K562	blood:
3	chr3:142295888..142299099-chr3:142720440..142723490,3	K562	blood:
4	chr3:142442417..142444804-chr3:142718685..142721847,4	K562	blood:
5	chr3:142676730..142680278-chr3:142717890..142721546,3	K562	blood:
6	chr3:142442669..142444351-chr3:142720029..142722522,2	MCF-7	breast:
7	chr3:142297403..142299294-chr3:142720282..142722143,3	MCF-7	breast:
8	chr3:142295918..142298932-chr3:142719049..142722504,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268129	TF binding region
ENSG00000144935	Chromatin interaction
ENSG00000163710	Chromatin interaction
ENSG00000175054	Chromatin interaction
ENSG00000241592	Chromatin interaction
ENSG00000242390	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10413	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1043898	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10451867	0.83[EUR][1000 genomes]
rs10513184	0.84[EUR][1000 genomes]
rs1053950	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10790	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10935474	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10935475	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935479	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11915462	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11922201	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12485790	0.87[EUR][1000 genomes]
rs12490776	0.83[EUR][1000 genomes]
rs12492904	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12695770	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13075955	0.83[EUR][1000 genomes]
rs13094293	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1349262	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13715	0.85[EUR][1000 genomes]
rs1375814	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1449868	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1449869	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1530753	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1532588	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17557029	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1814565	0.90[EUR][1000 genomes]
rs1827159	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1839406	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1868569	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1868570	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1965343	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2045306	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2124541	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2124542	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2124543	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2137586	0.89[EUR][1000 genomes]
rs2175739	0.89[EUR][1000 genomes]
rs2290549	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2353408	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2353409	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2353411	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821645	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3856697	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3902877	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4030582	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683444	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4683721	0.88[EUR][1000 genomes]
rs4683722	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683723	0.83[EUR][1000 genomes]
rs4683724	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56382522	0.88[EUR][1000 genomes]
rs6440129	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440131	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440132	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6440133	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6440134	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6770102	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6778454	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6781080	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6781887	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6783145	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6802376	0.82[EUR][1000 genomes]
rs6805417	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6806551	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6808689	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7611721	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7623532	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7644475	0.84[EUR][1000 genomes]
rs7648143	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7649225	0.82[EUR][1000 genomes]
rs7652745	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs766360	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs936194	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs936196	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs936197	0.83[EUR][1000 genomes]
rs937498	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9814656	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9816317	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9835348	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9847059	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9851353	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9862433	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9877128	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9877135	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][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	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv877563	chr3:142661350-142743889	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1545597	SR140	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142718200-142725000	Active TSS	K562	blood
2	chr3:142718400-142721800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:142718400-142722000	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr3:142718400-142722400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:142718600-142722200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr3:142718600-142722200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr3:142718800-142721800	Active TSS	Left Ventricle	heart
8	chr3:142718800-142722200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:142718800-142722400	Active TSS	H1 Cell Line	embryonic stem cell
10	chr3:142718800-142722400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:142718800-142722400	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:142718800-142723000	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr3:142719000-142721800	Active TSS	Right Atrium	heart
14	chr3:142719000-142722000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr3:142719000-142722200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:142719000-142722200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:142719000-142722200	Active TSS	HSMMtube	muscle
18	chr3:142719000-142722800	Active TSS	A549	lung
19	chr3:142719200-142721600	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr3:142719200-142721800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr3:142719200-142721800	Active TSS	Ovary	ovary
22	chr3:142719200-142722000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:142719200-142722000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:142719200-142722200	Active TSS	NHLF	lung
25	chr3:142719200-142723400	Active TSS	GM12878-XiMat	blood
26	chr3:142719400-142721600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:142719400-142721600	Active TSS	Gastric	stomach
28	chr3:142719400-142721600	Active TSS	Lung	lung
29	chr3:142719400-142721800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:142719400-142721800	Active TSS	Esophagus	oesophagus
31	chr3:142719400-142722000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:142719400-142722000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:142719400-142722000	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr3:142719400-142722000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:142719400-142722000	Active TSS	Fetal Intestine Large	intestine
36	chr3:142719400-142722200	Active TSS	Hela-S3	cervix
37	chr3:142719400-142722200	Active TSS	NHDF-Ad	bronchial
38	chr3:142719400-142722400	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr3:142719400-142722400	Active TSS	NHEK	skin
40	chr3:142719600-142721600	Active TSS	Colonic Mucosa	Colon
41	chr3:142719600-142721600	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr3:142719600-142721600	Active TSS	Pancreas	Pancrea
43	chr3:142719600-142721600	Active TSS	Placenta Amnion	Placenta Amnion
44	chr3:142719600-142721600	Active TSS	Stomach Mucosa	stomach
45	chr3:142719600-142721600	Active TSS	Osteobl	bone
46	chr3:142719600-142721800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:142719600-142721800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:142719600-142721800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:142719600-142721800	Active TSS	Fetal Muscle Trunk	muscle
50	chr3:142719600-142722000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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