Variant report

Variant	rs7133314
Chromosome Location	chr12:51664512-51664513
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	chr12:51662895-51665050	SK-N-SH	brain:	n/a	chr12:51663487-51663505 chr12:51664248-51664269 chr12:51664255-51664268 chr12:51663212-51663233 chr12:51663489-51663510 chr12:51663641-51663654 chr12:51663490-51663499 chr12:51664253-51664271
2	MAX	chr12:51663212-51664801	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:51663835-51665220	HUVEC	blood vessel:	n/a	n/a
4	TCF12	chr12:51663245-51664924	ECC-1	luminal epithelium:	n/a	chr12:51663493-51663500 chr12:51664606-51664613 chr12:51663955-51663962
5	SIN3AK20	chr12:51664337-51664701	A549	lung:	n/a	n/a
6	POLR2A	chr12:51663444-51664712	A549	lung:	n/a	n/a
7	MAZ	chr12:51663380-51665099	IMR90	lung:	n/a	n/a
8	TBP	chr12:51664253-51664742	HepG2	liver:	n/a	n/a
9	MAX	chr12:51663069-51664971	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr12:51664341-51664736	HepG2	liver:	n/a	n/a
11	TAF1	chr12:51663803-51664629	K562	blood:	n/a	n/a
12	FOSL2	chr12:51664164-51665212	A549	lung:	n/a	chr12:51664212-51664221 chr12:51664913-51664923 chr12:51664913-51664923 chr12:51664862-51664873 chr12:51664913-51664923
13	MXI1	chr12:51663886-51664808	HepG2	liver:	n/a	n/a
14	MYC	chr12:51664404-51665056	MCF10A-Er-Src	breast:	n/a	n/a
15	SP1	chr12:51663115-51665261	HCT-116	colon:	n/a	chr12:51664015-51664026 chr12:51664015-51664027 chr12:51664205-51664217 chr12:51664105-51664114 chr12:51664206-51664215 chr12:51664015-51664027 chr12:51664202-51664216 chr12:51664206-51664216 chr12:51664205-51664217
16	SMARCC1	chr12:51664288-51665172	Hela-S3	cervix:	n/a	n/a
17	MAX	chr12:51663106-51665113	ECC-1	luminal epithelium:	n/a	n/a
18	UBTF	chr12:51663405-51664681	K562	blood:	n/a	n/a
19	HEY1	chr12:51664428-51664783	HepG2	liver:	n/a	n/a
20	POLR2A	chr12:51663903-51665135	SK-N-SH	brain:	n/a	n/a
21	ZBTB7A	chr12:51663251-51665153	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr12:51664477-51664665	A549	lung:	n/a	n/a
23	TAF1	chr12:51663862-51665031	Hela-S3	cervix:	n/a	n/a
24	GATA3	chr12:51663861-51664916	MCF-7	breast:	n/a	chr12:51664862-51664871 chr12:51664879-51664889
25	POLR2A	chr12:51663831-51665027	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr12:51663932-51665310	U87	brain:	n/a	n/a
27	POLR2A	chr12:51663460-51665069	HepG2	liver:	n/a	n/a
28	MXI1	chr12:51663822-51665148	IMR90	lung:	n/a	n/a
29	POLR2A	chr12:51664456-51664688	A549	lung:	n/a	n/a
30	RAD21	chr12:51664309-51665039	IMR90	lung:	n/a	n/a
31	RCOR1	chr12:51663877-51665169	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr12:51663779-51665176	Hela-S3	cervix:	n/a	n/a
33	MAX	chr12:51662585-51665505	HCT-116	colon:	n/a	n/a
34	MXI1	chr12:51664022-51665001	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr12:51663406-51665111	Hela-S3	cervix:	n/a	n/a
36	GATA3	chr12:51664487-51664887	T-47D	breast:	n/a	chr12:51664862-51664871
37	EGR1	chr12:51663192-51664541	ECC-1	luminal epithelium:	n/a	chr12:51664012-51664025 chr12:51663641-51663651 chr12:51664103-51664112 chr12:51663640-51663650 chr12:51663640-51663653 chr12:51663864-51663877 chr12:51663550-51663560 chr12:51663545-51663558
38	MAX	chr12:51663373-51665060	Hela-S3	cervix:	n/a	n/a
39	EGR1	chr12:51663164-51665263	HCT-116	colon:	n/a	chr12:51664012-51664025 chr12:51663641-51663651 chr12:51664103-51664112 chr12:51663640-51663650 chr12:51663640-51663653 chr12:51663864-51663877 chr12:51663550-51663560 chr12:51663545-51663558
40	MAZ	chr12:51663285-51664761	K562	blood:	n/a	n/a
41	MAZ	chr12:51664455-51664730	HepG2	liver:	n/a	n/a
42	SP1	chr12:51663843-51665238	A549	lung:	n/a	chr12:51664015-51664026 chr12:51664015-51664027 chr12:51664205-51664217 chr12:51664105-51664114 chr12:51664206-51664215 chr12:51664015-51664027 chr12:51664202-51664216 chr12:51664206-51664216 chr12:51664205-51664217
43	MAX	chr12:51663256-51664947	A549	lung:	n/a	n/a
44	POLR2A	chr12:51664423-51664718	HepG2	liver:	n/a	n/a
45	POLR2A	chr12:51663878-51665398	U87	brain:	n/a	n/a
46	FOS	chr12:51664270-51665161	HUVEC	blood vessel:	n/a	chr12:51664913-51664923 chr12:51664913-51664923 chr12:51664862-51664873 chr12:51664913-51664923
47	HMGN3	chr12:51663409-51664658	K562	blood:	n/a	n/a
48	CHD2	chr12:51664455-51664535	GM12878	blood:	n/a	n/a
49	SMARCB1	chr12:51663171-51664948	Hela-S3	cervix:	n/a	n/a
50	CREB1	chr12:51663237-51664855	HepG2	liver:	n/a	chr12:51663478-51663491

No.	Distal block	Cell Line	Cell type
1	chr12:51664068..51664576-chr8:103876150..103876665,2	Hela-S3	cervix:
2	chr12:51476120..51478171-chr12:51663790..51665919,2	MCF-7	breast:
3	chr1:210547164..210547723-chr12:51663910..51664553,2	Hela-S3	cervix:
4	chr12:51661913..51666807-chr12:51714627..51721165,8	MCF-7	breast:
5	chr12:51416514..51419391-chr12:51663583..51665592,2	MCF-7	breast:
6	chr12:51440322..51443098-chr12:51662230..51665433,4	K562	blood:
7	chr12:51440784..51442942-chr12:51664189..51666029,2	MCF-7	breast:
8	chr12:51475968..51477695-chr12:51663580..51665438,2	MCF-7	breast:
9	chr12:51631526..51635212-chr12:51662486..51664929,4	MCF-7	breast:
10	chr12:51664358..51665286-chr9:117349629..117350181,2	Hela-S3	cervix:
11	chr12:51661897..51665217-chr12:51739188..51742261,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DAZAP2-4	chr12:51664502-51665144	NONHSAT028251
2	lnc-DAZAP2-4	chr12:51664502-51665081	NONHSAT028252

Variant related genes	Relation type
SMAGP	TF binding region
ENSG00000136888	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000253320	Chromatin interaction
ENSG00000110934	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000139610	Chromatin interaction
ENSG00000155096	Chromatin interaction
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10783427	0.80[CEU][hapmap]
rs10876156	0.93[CEU][hapmap]
rs1130641	0.93[CEU][hapmap]
rs11341	0.85[CEU][hapmap]
rs1362963	0.81[ASW][hapmap];0.86[CEU][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.86[YRI][hapmap]
rs17860299	0.92[TSI][hapmap]
rs17860317	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs1991433	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114876	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288367	0.93[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2359450	0.81[EUR][1000 genomes]
rs3210837	0.81[ASW][hapmap];0.86[CEU][hapmap];0.86[YRI][hapmap]
rs3858637	0.85[CEU][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs3969069	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4477479	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611251	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4761815	0.80[CEU][hapmap]
rs4761935	0.80[CEU][hapmap]
rs4761981	0.80[CEU][hapmap]
rs4761982	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4761985	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4761994	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4761995	0.80[CEU][hapmap]
rs6580820	0.80[CEU][hapmap]
rs6580821	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135736	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306875	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7308177	0.81[EUR][1000 genomes]
rs7311196	0.84[CEU][hapmap];0.92[TSI][hapmap]
rs7312857	0.85[CEU][hapmap];0.92[TSI][hapmap]
rs7316221	0.81[EUR][1000 genomes]
rs7316433	0.93[CEU][hapmap];0.84[TSI][hapmap]
rs7316604	0.81[EUR][1000 genomes]
rs74093810	0.81[EUR][1000 genomes]
rs74093814	0.81[EUR][1000 genomes]
rs7954976	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957868	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7975715	0.81[EUR][1000 genomes]
rs9795976	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv3405622	chr12:51662910-51665458	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51661000-51665000	Active TSS	Colonic Mucosa	Colon
2	chr12:51661400-51664800	Active TSS	Esophagus	oesophagus
3	chr12:51661600-51664600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:51662600-51664600	Active TSS	Sigmoid Colon	Sigmoid Colon
5	chr12:51662800-51664600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:51662800-51664600	Active TSS	Gastric	stomach
7	chr12:51662800-51664800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr12:51662800-51664800	Bivalent/Poised TSS	Fetal Stomach	stomach
9	chr12:51662800-51664800	Active TSS	Ovary	ovary
10	chr12:51662800-51665000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr12:51662800-51665000	Active TSS	Left Ventricle	heart
12	chr12:51662800-51665000	Active TSS	Right Atrium	heart
13	chr12:51662800-51665000	Active TSS	Right Ventricle	heart
14	chr12:51662800-51665000	Active TSS	Small Intestine	intestine
15	chr12:51662800-51665400	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr12:51663000-51664600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chr12:51663000-51664600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
18	chr12:51663000-51664600	Active TSS	Brain Anterior Caudate	brain
19	chr12:51663000-51664600	Active TSS	NHLF	lung
20	chr12:51663000-51664600	Active TSS	Osteobl	bone
21	chr12:51663000-51665000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:51663000-51665000	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr12:51663000-51665200	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr12:51663200-51664600	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr12:51663200-51664600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:51663200-51664600	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr12:51663200-51664800	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr12:51663200-51664800	Active TSS	Brain Angular Gyrus	brain
29	chr12:51663200-51664800	Active TSS	Colon Smooth Muscle	Colon
30	chr12:51663400-51664600	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr12:51663400-51664600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:51663400-51664600	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr12:51663400-51664600	Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr12:51663400-51664600	Active TSS	Aorta	Aorta
35	chr12:51663400-51664600	Active TSS	Liver	Liver
36	chr12:51663400-51664600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:51663400-51664600	Active TSS	HepG2	liver
38	chr12:51663400-51664800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:51663400-51664800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:51663400-51664800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:51663400-51664800	Active TSS	Brain Hippocampus Middle	brain
42	chr12:51663400-51664800	Active TSS	A549	lung
43	chr12:51663400-51664800	Active TSS	Hela-S3	cervix
44	chr12:51663400-51665000	Active TSS	NHDF-Ad	bronchial
45	chr12:51663400-51665200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:51663600-51664600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:51663600-51664600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:51663600-51664600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:51663600-51664600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:51663600-51664600	Active TSS	Lung	lung

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