Variant report

Variant	rs6581580
Chromosome Location	chr12:65002969-65002970
allele	G/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	STAT3	chr12:65002712-65003219	Hela-S3	cervix:	n/a	chr12:65002881-65002890 chr12:65002880-65002889
2	USF1	chr12:65002419-65003137	A549	lung:	n/a	n/a
3	RCOR1	chr12:65002577-65003637	K562	blood:	n/a	n/a
4	USF2	chr12:65002233-65003165	Hela-S3	cervix:	n/a	chr12:65002783-65002794
5	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
6	ATF3	chr12:65002635-65003090	K562	blood:	n/a	n/a
7	CTCF	chr12:65002799-65003216	IMR90	lung:	n/a	n/a
8	RFX5	chr12:65002845-65003164	K562	blood:	n/a	n/a
9	MTA3	chr12:65002578-65004147	GM12878	blood:	n/a	n/a
10	CTCF	chr12:65002960-65003110	HEK293	kidney:	n/a	n/a
11	CTCF	chr12:65002880-65003030	SAEC	small airway:	n/a	n/a
12	USF1	chr12:65002572-65003003	K562	blood:	n/a	n/a
13	HEY1	chr12:65002620-65003125	K562	blood:	n/a	n/a
14	HEY1	chr12:65002633-65003224	HepG2	liver:	n/a	n/a
15	MYBL2	chr12:65002596-65003187	HepG2	liver:	n/a	n/a
16	USF2	chr12:65002605-65003204	GM12878	blood:	n/a	chr12:65002783-65002794
17	REST	chr12:65002543-65004065	A549	lung:	n/a	chr12:65003908-65003921 chr12:65003581-65003601
18	YY1	chr12:65002646-65003187	GM12891	blood:	n/a	n/a
19	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
20	FOS	chr12:65002647-65003126	MCF10A-Er-Src	breast:	n/a	chr12:65002879-65002891 chr12:65002881-65002888 chr12:65002879-65002890 chr12:65002880-65002889 chr12:65002881-65002889 chr12:65002880-65002890
21	POLR2A	chr12:65002578-65005353	GM12892	blood:	n/a	n/a
22	MXI1	chr12:65002626-65003158	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:65002570-65003286	GM12891	blood:	n/a	n/a
24	POLR2A	chr12:65002580-65006225	GM18505	blood:	n/a	n/a
25	POLR2A	chr12:65002768-65003092	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr12:65002696-65005109	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr12:65002613-65003212	GM12891	blood:	n/a	n/a
28	TAF1	chr12:65002716-65003080	Hela-S3	cervix:	n/a	n/a
29	KAT2A	chr12:65002914-65003035	GM12878	blood:	n/a	n/a
30	YY1	chr12:65002591-65003200	GM12878	blood:	n/a	n/a
31	CTCF	chr12:65002880-65003030	RPTEC	kidney:	n/a	n/a
32	TAF1	chr12:65002687-65003112	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr12:65002217-65006352	K562	blood:	n/a	n/a
34	CTCF	chr12:65001972-65003394	K562	blood:	n/a	n/a
35	JUN	chr12:65002744-65003018	HepG2	liver:	n/a	chr12:65002879-65002891 chr12:65002881-65002888 chr12:65002880-65002889 chr12:65002881-65002889 chr12:65002880-65002890
36	POLR2A	chr12:65002553-65004955	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr12:65002733-65003121	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr12:65002880-65003030	HCM	heart:	n/a	n/a
39	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
40	CTCF	chr12:65002840-65002990	HFF	foreskin:	n/a	n/a
41	MAZ	chr12:65002028-65005354	Hela-S3	cervix:	n/a	chr12:65002881-65002890 chr12:65002880-65002889 chr12:65003947-65003957 chr12:65004589-65004599
42	PML	chr12:65002401-65005958	GM12878	blood:	n/a	chr12:65002561-65002569 chr12:65002879-65002888
43	STAT3	chr12:65002506-65003362	MCF10A-Er-Src	breast:	n/a	chr12:65002674-65002682 chr12:65002881-65002890 chr12:65002880-65002889
44	ARID3A	chr12:65001932-65003917	K562	blood:	n/a	n/a
45	MYC	chr12:65002886-65002975	GM12878	blood:	n/a	n/a
46	SIN3AK20	chr12:65002585-65003263	A549	lung:	n/a	n/a
47	SMC3	chr12:65001972-65004063	Hela-S3	cervix:	n/a	chr12:65003364-65003371 chr12:65003950-65003960
48	FOSL2	chr12:65002398-65003410	A549	lung:	n/a	chr12:65002879-65002891 chr12:65002878-65002889 chr12:65002881-65002888 chr12:65002880-65002889 chr12:65002881-65002889 chr12:65002880-65002890
49	CTCF	chr12:65002882-65003127	GM12892	blood:	n/a	n/a
50	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

No.	Distal block	Cell Line	Cell type
1	chr12:65001714..65006897-chr12:65088342..65093997,11	MCF-7	breast:
2	chr12:65002574..65003271-chr4:103789942..103790730,2	Hela-S3	cervix:
3	chr12:64796628..64799812-chr12:65002415..65005896,3	K562	blood:
4	chr12:65002667..65003975-chr15:72523179..72524331,3	Hela-S3	cervix:
5	chr12:65002395..65003289-chr7:75543806..75544708,2	NB4	blood:
6	chr12:65002182..65006670-chr12:65087134..65093452,10	MCF-7	breast:
7	chr12:64796580..64799507-chr12:65002415..65006757,4	K562	blood:
8	chr12:65001959..65005152-chr12:65021514..65024393,3	K562	blood:
9	chr12:64990517..64993070-chr12:65001225..65003160,2	MCF-7	breast:
10	chr12:64844835..64848934-chr12:65001187..65005448,7	MCF-7	breast:
11	chr12:65001959..65007139-chr12:65021874..65025265,5	K562	blood:
12	chr12:64844696..64847501-chr12:65001513..65004366,3	K562	blood:
13	chr12:65001526..65007900-chr12:65015799..65021807,8	K562	blood:
14	chr12:65001678..65008078-chr12:65013108..65023657,17	MCF-7	breast:

Variant related genes	Relation type
RASSF3	TF binding region
ENSG00000183735	Chromatin interaction
ENSG00000067225	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000184575	Chromatin interaction
ENSG00000207546	Chromatin interaction
ENSG00000265020	Chromatin interaction
ENSG00000127948	Chromatin interaction
ENSG00000268028	Chromatin interaction
ENSG00000225195	Chromatin interaction
ENSG00000145354	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10784415	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3741747	0.85[ASN][1000 genomes]
rs3741748	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964093	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6581579	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][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	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

No data

Chromatin state (count:124 , 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	chr12:65002200-65003000	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr12:65002200-65004000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr12:65002400-65003000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:65002400-65003000	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr12:65002400-65003200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:65002400-65003400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr12:65002400-65003800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr12:65002400-65003800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr12:65002400-65003800	Flanking Active TSS	HUVEC	blood vessel
13	chr12:65002400-65004400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:65002400-65005400	Active TSS	K562	blood
15	chr12:65002400-65006000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:65002400-65006000	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr12:65002400-65006200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:65002400-65006400	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr12:65002600-65003000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:65002600-65003000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
21	chr12:65002600-65003000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr12:65002600-65003000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr12:65002600-65003000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:65002600-65003000	Enhancers	Small Intestine	intestine
25	chr12:65002600-65003200	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:65002600-65003200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:65002600-65003200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr12:65002600-65003200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:65002600-65003200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:65002600-65003200	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr12:65002600-65003200	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr12:65002600-65003400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:65002600-65003400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr12:65002600-65003400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr12:65002600-65003600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:65002600-65003600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr12:65002600-65003600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr12:65002600-65003800	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr12:65002600-65003800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:65002600-65003800	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr12:65002600-65003800	Flanking Active TSS	Fetal Thymus	thymus
42	chr12:65002600-65003800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr12:65002600-65004000	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr12:65002600-65004000	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr12:65002600-65004000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:65002600-65004000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:65002600-65005200	Active TSS	Brain Cingulate Gyrus	brain
48	chr12:65002600-65005600	Active TSS	Fetal Intestine Large	intestine
49	chr12:65002600-65005600	Active TSS	Fetal Lung	lung
50	chr12:65002600-65005800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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