Variant report

Variant	rs1716518
Chromosome Location	chr12:65049252-65049253
allele	A/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	TAL1	chr12:65048971-65049297	K562	blood:	n/a	n/a
2	FOS	chr12:65048958-65049286	MCF10A-Er-Src	breast:	n/a	n/a
3	FOXA1	chr12:65048899-65049284	HepG2	liver:	n/a	n/a
4	CEBPB	chr12:65048910-65049272	IMR90	lung:	n/a	chr12:65049095-65049106 chr12:65049094-65049107
5	TEAD4	chr12:65048896-65049256	K562	blood:	n/a	n/a
6	FOS	chr12:65049001-65049329	MCF10A-Er-Src	breast:	n/a	n/a
7	HDAC2	chr12:65048969-65049277	HepG2	liver:	n/a	chr12:65048991-65049000
8	CEBPB	chr12:65048853-65049292	A549	lung:	n/a	chr12:65049095-65049106 chr12:65049094-65049107
9	CEBPB	chr12:65048899-65049262	A549	lung:	n/a	chr12:65049095-65049106 chr12:65049094-65049107
10	RCOR1	chr12:65048762-65049275	K562	blood:	n/a	n/a
11	CEBPB	chr12:65048855-65049338	K562	blood:	n/a	chr12:65049095-65049106 chr12:65049094-65049107
12	EP300	chr12:65048915-65049280	HepG2	liver:	n/a	n/a
13	FOS	chr12:65049029-65049286	MCF10A-Er-Src	breast:	n/a	n/a
14	CEBPB	chr12:65048773-65049387	A549	lung:	n/a	chr12:65049095-65049106 chr12:65049094-65049107
15	TEAD4	chr12:65048958-65049283	K562	blood:	n/a	n/a
16	MYBL2	chr12:65048764-65049286	HepG2	liver:	n/a	n/a
17	JUND	chr12:65049001-65049293	HepG2	liver:	n/a	n/a
18	CEBPB	chr12:65048883-65049282	K562	blood:	n/a	chr12:65049095-65049106 chr12:65049094-65049107
19	TEAD4	chr12:65048816-65049435	HepG2	liver:	n/a	n/a
20	ARID3A	chr12:65048844-65049289	HepG2	liver:	n/a	n/a
21	CEBPB	chr12:65048855-65049294	HepG2	liver:	n/a	chr12:65049095-65049106 chr12:65049094-65049107
22	CEBPB	chr12:65048950-65049287	HepG2	liver:	n/a	chr12:65049095-65049106 chr12:65049094-65049107
23	EP300	chr12:65048955-65049291	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000256314	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10748011	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11175496	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1147097	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1147104	0.91[EUR][1000 genomes]
rs1147106	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1244870	0.83[ASN][1000 genomes]
rs1244871	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1244872	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1244881	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1245170	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1261879	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1264239	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1270430	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1520766	0.80[EUR][1000 genomes]
rs1690261	0.82[CEU][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1716497	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1795614	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1795617	0.88[EUR][1000 genomes]
rs1797690	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1797699	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682713	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2682717	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682721	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4264239	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs572046	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs577303	0.82[CEU][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7307999	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7308397	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65025000-65059600	Weak transcription	Thymus	Thymus
2	chr12:65028600-65056400	Weak transcription	NHEK	skin
3	chr12:65033000-65052600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:65033600-65059400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:65038200-65051200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:65041400-65050400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr12:65041600-65052200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:65043600-65059600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:65044000-65059400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:65044200-65051400	Weak transcription	Colonic Mucosa	Colon
11	chr12:65044600-65051000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr12:65044800-65050200	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:65044800-65050400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr12:65045000-65051000	Weak transcription	GM12878-XiMat	blood
15	chr12:65045200-65050200	Enhancers	Primary T cells from cord blood	blood
16	chr12:65045600-65054600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:65045800-65051000	Weak transcription	Gastric	stomach
18	chr12:65045800-65056400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:65046400-65050200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr12:65046400-65058600	Weak transcription	Ovary	ovary
21	chr12:65046600-65050200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr12:65046600-65051800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:65046800-65049800	Weak transcription	HUVEC	blood vessel
24	chr12:65046800-65050000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:65046800-65050000	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr12:65047000-65049800	Enhancers	Placenta	Placenta
27	chr12:65047000-65050800	Weak transcription	Right Atrium	heart
28	chr12:65047000-65051400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr12:65047000-65056400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr12:65047000-65059400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:65047200-65051200	Weak transcription	Spleen	Spleen
32	chr12:65047200-65059400	Weak transcription	Fetal Stomach	stomach
33	chr12:65047400-65059400	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr12:65047800-65049600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr12:65047800-65050400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:65047800-65050600	Weak transcription	Colon Smooth Muscle	Colon
37	chr12:65047800-65050800	Weak transcription	Lung	lung
38	chr12:65047800-65051200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:65047800-65051600	Weak transcription	Aorta	Aorta
40	chr12:65047800-65051600	Weak transcription	Right Ventricle	heart
41	chr12:65047800-65051800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:65047800-65052600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:65047800-65056000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:65047800-65056400	Weak transcription	Hela-S3	cervix
45	chr12:65047800-65056600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:65047800-65059400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:65047800-65059400	Weak transcription	NHLF	lung
48	chr12:65047800-65063000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:65048000-65050600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:65048000-65051200	Weak transcription	HMEC	breast

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