Variant report

Variant	rs7961565
Chromosome Location	chr12:118559141-118559142
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	MYBL2	chr12:118558632-118559296	HepG2	liver:	n/a	n/a
2	RAD21	chr12:118558300-118559294	SK-N-SH	brain:	n/a	chr12:118558845-118558864
3	JUND	chr12:118558257-118559332	H1-hESC	embryonic stem cell:	n/a	chr12:118558815-118558824 chr12:118558811-118558820 chr12:118558824-118558833 chr12:118558824-118558834 chr12:118558824-118558834 chr12:118558814-118558823 chr12:118558824-118558834 chr12:118558824-118558834
4	RAD21	chr12:118558594-118559152	HepG2	liver:	n/a	chr12:118558845-118558864
5	RAD21	chr12:118558638-118559162	A549	lung:	n/a	chr12:118558845-118558864
6	CEBPB	chr12:118558760-118559180	HepG2	liver:	n/a	n/a
7	RAD21	chr12:118558663-118559153	A549	lung:	n/a	chr12:118558845-118558864
8	FOXA1	chr12:118558772-118559225	HepG2	liver:	n/a	n/a
9	FOXA1	chr12:118558796-118559244	HepG2	liver:	n/a	n/a
10	CTCF	chr12:118559000-118559150	AG04449	skin:	n/a	n/a
11	CTCF	chr12:118558634-118559197	HCT-116	colon:	n/a	chr12:118558844-118558862 chr12:118558846-118558867 chr12:118558849-118558859 chr12:118558845-118558861 chr12:118558847-118558860
12	CTCF	chr12:118558493-118559266	K562	blood:	n/a	chr12:118558844-118558862 chr12:118558846-118558867 chr12:118558849-118558859 chr12:118558845-118558861 chr12:118558847-118558860
13	JUN	chr12:118558820-118559159	K562	blood:	n/a	chr12:118558824-118558833 chr12:118558824-118558834 chr12:118558824-118558834 chr12:118558824-118558834 chr12:118558824-118558834
14	EP300	chr12:118558702-118559180	HepG2	liver:	n/a	n/a
15	JUND	chr12:118558611-118559186	K562	blood:	n/a	chr12:118558815-118558824 chr12:118558811-118558820 chr12:118558824-118558833 chr12:118558824-118558834 chr12:118558824-118558834 chr12:118558814-118558823 chr12:118558824-118558834 chr12:118558824-118558834
16	SMC3	chr12:118558549-118559212	HepG2	liver:	n/a	chr12:118558850-118558860 chr12:118558758-118558766 chr12:118558846-118558860
17	CTCF	chr12:118558219-118559195	SK-N-SH	brain:	n/a	chr12:118558844-118558862 chr12:118558846-118558867 chr12:118558849-118558859 chr12:118558845-118558861 chr12:118558847-118558860
18	CUX1	chr12:118558324-118559146	K562	blood:	n/a	n/a
19	RCOR1	chr12:118558854-118559157	HepG2	liver:	n/a	n/a
20	TEAD4	chr12:118558650-118559361	HepG2	liver:	n/a	n/a
21	RAD21	chr12:118558459-118559274	HCT-116	colon:	n/a	chr12:118558845-118558864
22	RXRA	chr12:118558768-118559162	HepG2	liver:	n/a	chr12:118558783-118558805 chr12:118558844-118558864 chr12:118558893-118558902 chr12:118558784-118558803
23	MYC	chr12:118558580-118559234	K562	blood:	n/a	n/a
24	ELK1	chr12:118558849-118559190	K562	blood:	n/a	n/a
25	RAD21	chr12:118558610-118559169	HepG2	liver:	n/a	chr12:118558845-118558864
26	ESRRA	chr12:118558729-118559158	HepG2	liver:	n/a	chr12:118558892-118558902 chr12:118558787-118558806 chr12:118558890-118558906 chr12:118558892-118558902 chr12:118558894-118558912 chr12:118558890-118558902 chr12:118558782-118558801
27	RAD21	chr12:118558707-118559167	ECC-1	luminal epithelium:	n/a	chr12:118558845-118558864
28	CHD1	chr12:118558139-118559281	H1-hESC	embryonic stem cell:	n/a	chr12:118558817-118558827
29	RAD21	chr12:118558665-118559295	Hela-S3	cervix:	n/a	chr12:118558845-118558864
30	CTCF	chr12:118559140-118559290	HRPEpiC	eye:	n/a	n/a
31	SP1	chr12:118558811-118559197	HepG2	liver:	n/a	chr12:118558812-118558826 chr12:118558815-118558827 chr12:118558816-118558826 chr12:118558817-118558826 chr12:118558816-118558826 chr12:118558815-118558827 chr12:118558817-118558826 chr12:118558816-118558825
32	ZNF143	chr12:118558745-118559213	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr12:118558204-118559556	A549	lung:	n/a	chr12:118558844-118558862 chr12:118558846-118558867 chr12:118558849-118558859 chr12:118558845-118558861 chr12:118558847-118558860
34	RAD21	chr12:118558625-118559169	HCT-116	colon:	n/a	chr12:118558845-118558864
35	ARID3A	chr12:118558756-118559264	HepG2	liver:	n/a	n/a
36	ESRRA	chr12:118558146-118559414	GM12878	blood:	n/a	chr12:118558892-118558902 chr12:118558787-118558806 chr12:118558890-118558906 chr12:118558892-118558902 chr12:118558894-118558912 chr12:118558890-118558902 chr12:118558782-118558801
37	EP300	chr12:118558709-118559201	HepG2	liver:	n/a	n/a
38	CTCF	chr12:118559080-118559230	GM12871	blood:	n/a	n/a
39	RAD21	chr12:118558659-118559150	ECC-1	luminal epithelium:	n/a	chr12:118558845-118558864
40	SMC3	chr12:118558533-118559150	GM12878	blood:	n/a	chr12:118558850-118558860 chr12:118558758-118558766 chr12:118558846-118558860

No.	Distal block	Cell Line	Cell type
1	chr12:118497477..118500466-chr12:118559121..118561956,3	MCF-7	breast:
2	chr12:118558694..118561471-chr12:118568462..118574858,6	MCF-7	breast:
3	chr12:118558384..118559345-chr12:118813588..118814202,2	MCF-7	breast:
4	chr12:118558538..118559185-chr12:118813580..118814462,3	K562	blood:
5	chr12:118557596..118560350-chr12:118572704..118574934,3	MCF-7	breast:
6	chr12:118498692..118501195-chr12:118558625..118560440,2	MCF-7	breast:
7	chr12:118539824..118542719-chr12:118557194..118560231,3	MCF-7	breast:

Variant related genes	Relation type
VSIG10	TF binding region
ENSG00000270482	Chromatin interaction
ENSG00000089220	Chromatin interaction
ENSG00000176834	Chromatin interaction
ENSG00000176871	Chromatin interaction
ENSG00000111707	Chromatin interaction

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

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

rs_ID	r²[population]
rs10466936	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10466937	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34010869	0.83[EUR][1000 genomes]
rs3858532	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71452636	0.80[EUR][1000 genomes]
rs7300114	0.80[EUR][1000 genomes]
rs7973195	0.91[EUR][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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv560389	chr12:118502467-118564087	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv899546	chr12:118515230-118563982	Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118542400-118559200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:118542400-118562400	Weak transcription	Fetal Muscle Leg	muscle
3	chr12:118542400-118569400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:118542600-118569400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:118542600-118572800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr12:118542600-118573400	Weak transcription	Primary T cells from cord blood	blood
7	chr12:118545400-118569600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:118546400-118569400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:118548600-118563400	Weak transcription	Left Ventricle	heart
10	chr12:118552400-118561400	Weak transcription	Fetal Stomach	stomach
11	chr12:118552800-118572800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:118552800-118573400	Weak transcription	Aorta	Aorta
13	chr12:118553000-118573000	Weak transcription	Fetal Brain Female	brain
14	chr12:118554200-118560400	Weak transcription	Spleen	Spleen
15	chr12:118554200-118561400	Weak transcription	Pancreas	Pancrea
16	chr12:118554400-118566000	Weak transcription	Small Intestine	intestine
17	chr12:118554800-118564000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:118557600-118559200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:118557800-118564000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:118558200-118559200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:118558200-118559200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:118558200-118559200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:118558200-118559200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:118558200-118559200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:118558200-118559200	Enhancers	GM12878-XiMat	blood
26	chr12:118558200-118559200	Enhancers	HSMM	muscle
27	chr12:118558200-118559200	Enhancers	NHDF-Ad	bronchial
28	chr12:118558200-118559400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:118558200-118559400	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr12:118558200-118559400	Enhancers	Hela-S3	cervix
31	chr12:118558200-118559600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr12:118558200-118564000	Enhancers	HepG2	liver
33	chr12:118558400-118559200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:118558400-118559200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr12:118558400-118559200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr12:118558400-118559200	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr12:118558400-118559200	Enhancers	Muscle Satellite Cultured Cells	--
38	chr12:118558400-118559200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:118558400-118559200	Enhancers	Adipose Nuclei	Adipose
40	chr12:118558400-118559200	Enhancers	Brain Hippocampus Middle	brain
41	chr12:118558400-118559200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:118558400-118559200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr12:118558400-118559200	Enhancers	Fetal Intestine Large	intestine
44	chr12:118558400-118559200	Enhancers	Fetal Intestine Small	intestine
45	chr12:118558400-118559200	Enhancers	Fetal Kidney	kidney
46	chr12:118558400-118559200	Enhancers	Fetal Lung	lung
47	chr12:118558400-118559200	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr12:118558400-118559200	Enhancers	Dnd41	blood
49	chr12:118558400-118559200	Enhancers	HMEC	breast
50	chr12:118558400-118559200	Enhancers	HUVEC	blood vessel

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