Variant report

Variant	rs3741748
Chromosome Location	chr12:65004387-65004388
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	CTCF	chr12:65004240-65004390	GM12865	blood:	n/a	n/a
2	RAD21	chr12:65004292-65004917	IMR90	lung:	n/a	chr12:65004847-65004856 chr12:65004789-65004803 chr12:65004586-65004596
3	SMARCC1	chr12:65004275-65005964	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr12:65003629-65005274	GM12891	blood:	n/a	n/a
5	POLR2A	chr12:65003734-65005363	NB4	blood:	n/a	n/a
6	YY1	chr12:65004261-65004942	ECC-1	luminal epithelium:	n/a	chr12:65004283-65004297 chr12:65004582-65004596
7	MYC	chr12:65002007-65005666	K562	blood:	n/a	chr12:65002881-65002890 chr12:65002783-65002793 chr12:65002880-65002889 chr12:65003947-65003957 chr12:65005352-65005362 chr12:65004589-65004599
8	TAF1	chr12:65003864-65004487	K562	blood:	n/a	n/a
9	RAD21	chr12:65004368-65005178	ECC-1	luminal epithelium:	n/a	chr12:65004847-65004856 chr12:65004789-65004803 chr12:65005015-65005024 chr12:65004586-65004596
10	MAX	chr12:65002053-65006035	NB4	blood:	n/a	chr12:65002881-65002890 chr12:65002783-65002793 chr12:65002880-65002889 chr12:65003947-65003957 chr12:65005352-65005362 chr12:65004589-65004599
11	POLR2A	chr12:65002578-65005353	GM12892	blood:	n/a	n/a
12	YY1	chr12:65003614-65005120	GM12892	blood:	n/a	chr12:65004283-65004297 chr12:65004582-65004596
13	POLR2A	chr12:65002580-65006225	GM18505	blood:	n/a	n/a
14	MAX	chr12:65003804-65005013	SK-N-SH	brain:	n/a	chr12:65003947-65003957 chr12:65004589-65004599
15	POLR2A	chr12:65002696-65005109	Hela-S3	cervix:	n/a	n/a
16	MAX	chr12:65004330-65005106	HepG2	liver:	n/a	chr12:65004589-65004599
17	POLR2A	chr12:65003704-65005095	PANC-1	pancreas:	n/a	n/a
18	NFIC	chr12:65003450-65005406	ECC-1	luminal epithelium:	n/a	n/a
19	YY1	chr12:65003761-65004467	HepG2	liver:	n/a	chr12:65004283-65004297
20	NR2F2	chr12:65003385-65005504	MCF-7	breast:	n/a	n/a
21	STAT5A	chr12:65004343-65005382	GM12878	blood:	n/a	chr12:65004997-65005009 chr12:65005298-65005318
22	POLR2A	chr12:65002217-65006352	K562	blood:	n/a	n/a
23	TCF3	chr12:65003938-65005042	GM12878	blood:	n/a	n/a
24	SIN3AK20	chr12:65003646-65005043	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr12:65004343-65005101	U87	brain:	n/a	n/a
26	MAX	chr12:65003351-65005448	HepG2	liver:	n/a	chr12:65003947-65003957 chr12:65005352-65005362 chr12:65004589-65004599
27	MAX	chr12:65003792-65005539	ECC-1	luminal epithelium:	n/a	chr12:65003947-65003957 chr12:65005352-65005362 chr12:65004589-65004599
28	POLR2A	chr12:65002553-65004955	MCF10A-Er-Src	breast:	n/a	n/a
29	MYC	chr12:65004208-65004450	MCF-7	breast:	n/a	n/a
30	SIN3A	chr12:65004335-65005347	GM12878	blood:	n/a	chr12:65004538-65004547
31	POLR2A	chr12:65003865-65004964	IMR90	lung:	n/a	n/a
32	TAF1	chr12:65003830-65004497	HepG2	liver:	n/a	n/a
33	MAX	chr12:65002042-65005472	Hela-S3	cervix:	n/a	chr12:65002881-65002890 chr12:65002783-65002793 chr12:65002880-65002889 chr12:65003947-65003957 chr12:65005352-65005362 chr12:65004589-65004599
34	MAZ	chr12:65002028-65005354	Hela-S3	cervix:	n/a	chr12:65002881-65002890 chr12:65002880-65002889 chr12:65003947-65003957 chr12:65004589-65004599
35	TAF1	chr12:65004114-65005039	HepG2	liver:	n/a	n/a
36	PML	chr12:65002401-65005958	GM12878	blood:	n/a	chr12:65002561-65002569 chr12:65002879-65002888
37	POLR2A	chr12:65003549-65005333	K562	blood:	n/a	n/a
38	POLR2A	chr12:65003482-65005403	K562	blood:	n/a	n/a
39	MAX	chr12:65001741-65005431	HCT-116	colon:	n/a	chr12:65002881-65002890 chr12:65002783-65002793 chr12:65002880-65002889 chr12:65003947-65003957 chr12:65005352-65005362 chr12:65004589-65004599
40	POLR2A	chr12:65003819-65005474	HL-60	blood:	n/a	n/a
41	MYC	chr12:65003744-65005493	MCF10A-Er-Src	breast:	n/a	chr12:65003947-65003957 chr12:65005352-65005362 chr12:65004589-65004599
42	HDAC2	chr12:65003608-65005517	MCF-7	breast:	n/a	chr12:65005196-65005210
43	ZMIZ1	chr12:65002732-65004402	K562	blood:	n/a	n/a
44	POLR2A	chr12:65002577-65005426	GM12878	blood:	n/a	n/a
45	ELF1	chr12:65003589-65005248	MCF-7	breast:	n/a	chr12:65004536-65004548 chr12:65004282-65004294 chr12:65004281-65004293
46	IRF1	chr12:65003891-65004411	K562	blood:	n/a	chr12:65004095-65004109
47	POLR2A	chr12:65003492-65005040	HUVEC	blood vessel:	n/a	n/a
48	SRF	chr12:65003777-65005514	ECC-1	luminal epithelium:	n/a	chr12:65005199-65005213 chr12:65005200-65005213 chr12:65004100-65004110
49	POLR2A	chr12:65004173-65004413	GM12891	blood:	n/a	n/a
50	E2F1	chr12:65003923-65005067	Hela-S3	cervix:	n/a	chr12:65004584-65004593 chr12:65003953-65003962 chr12:65004762-65004777

No.	Distal block	Cell Line	Cell type
1	chr12:65001714..65006897-chr12:65088342..65093997,11	MCF-7	breast:
2	chr12:64796628..64799812-chr12:65002415..65005896,3	K562	blood:
3	chr1:28974934..28975572-chr12:65004207..65004918,2	Hela-S3	cervix:
4	chr12:65003563..65004407-chr8:21998747..21999449,2	Hela-S3	cervix:
5	chr12:65002182..65006670-chr12:65087134..65093452,10	MCF-7	breast:
6	chr12:64796580..64799507-chr12:65002415..65006757,4	K562	blood:
7	chr12:65001959..65005152-chr12:65021514..65024393,3	K562	blood:
8	chr12:64844835..64848934-chr12:65001187..65005448,7	MCF-7	breast:
9	chr12:65001959..65007139-chr12:65021874..65025265,5	K562	blood:
10	chr12:65001526..65007900-chr12:65015799..65021807,8	K562	blood:
11	chr12:65001678..65008078-chr12:65013108..65023657,17	MCF-7	breast:
12	chr12:65003158..65005716-chr12:65217154..65219440,2	MCF-7	breast:
13	chr12:49525114..49525857-chr12:65004032..65004831,2	Hela-S3	cervix:
14	chr1:202777265..202777801-chr12:65003536..65004412,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBK1-2	chr12:65004302-65004523	NONHSAT029155

Variant related genes	Relation type
ENSG00000256670	TF binding region
ENSG00000270103	Chromatin interaction
ENSG00000183735	Chromatin interaction
ENSG00000207546	Chromatin interaction
ENSG00000168476	Chromatin interaction
ENSG00000117139	Chromatin interaction
ENSG00000268028	Chromatin interaction
ENSG00000225195	Chromatin interaction
ENSG00000111490	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000184575	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10784415	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3741747	0.89[ASN][1000 genomes]
rs4964093	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6581579	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6581580	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7313651	0.82[AFR][1000 genomes]
rs7313765	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832443	chr12:64878856-65057265	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1048199	chr12:64951666-65021700	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
3	nsv541512	chr12:64951666-65021700	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
4	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv3384028	chr12:65003435-65005533	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65001800-65005400	Active TSS	Hela-S3	cervix
2	chr12:65001800-65006200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:65001800-65006600	Active TSS	A549	lung
4	chr12:65002400-65004400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:65002400-65005400	Active TSS	K562	blood
6	chr12:65002400-65006000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:65002400-65006000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr12:65002400-65006200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:65002400-65006400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr12:65002600-65005200	Active TSS	Brain Cingulate Gyrus	brain
11	chr12:65002600-65005600	Active TSS	Fetal Intestine Large	intestine
12	chr12:65002600-65005600	Active TSS	Fetal Lung	lung
13	chr12:65002600-65005800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:65002600-65006000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr12:65002600-65006000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:65002600-65006000	Active TSS	Fetal Intestine Small	intestine
17	chr12:65002600-65006000	Active TSS	HSMMtube	muscle
18	chr12:65002600-65006200	Active TSS	H9 Cell Line	embryonic stem cell
19	chr12:65002600-65006200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:65002600-65006200	Active TSS	Fetal Kidney	kidney
21	chr12:65002600-65006200	Active TSS	Fetal Muscle Trunk	muscle
22	chr12:65002600-65006200	Active TSS	HSMM	muscle
23	chr12:65002600-65006400	Active TSS	Right Ventricle	heart
24	chr12:65002600-65007000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:65002600-65007800	Active TSS	GM12878-XiMat	blood
26	chr12:65002800-65004400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:65002800-65004600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
28	chr12:65002800-65004800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:65002800-65004800	Active TSS	Thymus	Thymus
30	chr12:65002800-65005400	Active TSS	Brain Hippocampus Middle	brain
31	chr12:65002800-65005600	Active TSS	H1 Cell Line	embryonic stem cell
32	chr12:65002800-65005600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:65002800-65005600	Active TSS	Psoas Muscle	Psoas
34	chr12:65002800-65005600	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr12:65002800-65005600	Bivalent/Poised TSS	HepG2	liver
36	chr12:65002800-65005600	Active TSS	NHDF-Ad	bronchial
37	chr12:65002800-65005800	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr12:65002800-65005800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr12:65002800-65005800	Active TSS	Brain Angular Gyrus	brain
40	chr12:65002800-65005800	Active TSS	Brain Anterior Caudate	brain
41	chr12:65002800-65005800	Active TSS	Brain Substantia Nigra	brain
42	chr12:65002800-65005800	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr12:65002800-65005800	Active TSS	Gastric	stomach
44	chr12:65002800-65005800	Active TSS	Placenta Amnion	Placenta Amnion
45	chr12:65002800-65005800	Active TSS	Stomach Mucosa	stomach
46	chr12:65002800-65006000	Active TSS	Esophagus	oesophagus
47	chr12:65002800-65006000	Active TSS	Pancreas	Pancrea
48	chr12:65002800-65006000	Active TSS	NHLF	lung
49	chr12:65002800-65006200	Active TSS	Colonic Mucosa	Colon
50	chr12:65002800-65006200	Active TSS	Sigmoid Colon	Sigmoid Colon

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