Variant report

Variant	rs7959378
Chromosome Location	chr12:51567230-51567231
allele	A/C
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	TAF1	chr12:51565931-51567399	ECC-1	luminal epithelium:	n/a	n/a
2	CREB1	chr12:51566356-51567354	ECC-1	luminal epithelium:	n/a	chr12:51566917-51566930
3	GABPA	chr12:51565980-51567309	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr12:51566019-51567333	H1-hESC	embryonic stem cell:	n/a	n/a
5	JUN	chr12:51566629-51567241	H1-hESC	embryonic stem cell:	n/a	chr12:51566915-51566928 chr12:51566919-51566928
6	POLR2A	chr12:51565988-51567357	ECC-1	luminal epithelium:	n/a	n/a
7	TAF1	chr12:51566298-51567291	HepG2	liver:	n/a	n/a
8	GTF2B	chr12:51566399-51567246	K562	blood:	n/a	n/a
9	POLR2A	chr12:51566615-51567238	SK-N-MC	brain:	n/a	n/a
10	CCNT2	chr12:51566149-51567235	K562	blood:	n/a	chr12:51566615-51566624
11	POLR2A	chr12:51566311-51567361	HCT-116	colon:	n/a	n/a
12	POLR2A	chr12:51566254-51567389	PANC-1	pancreas:	n/a	n/a
13	GABPA	chr12:51566112-51567452	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr12:51566253-51567441	SK-N-MC	brain:	n/a	n/a
15	UBTF	chr12:51565787-51567286	K562	blood:	n/a	n/a
16	E2F6	chr12:51566372-51567397	A549	lung:	n/a	chr12:51566920-51566929 chr12:51566877-51566886 chr12:51566918-51566927
17	YY1	chr12:51566368-51567321	ECC-1	luminal epithelium:	n/a	chr12:51566871-51566893
18	JUN	chr12:51565435-51567459	K562	blood:	n/a	chr12:51566915-51566928 chr12:51566919-51566928
19	E2F4	chr12:51566382-51567251	K562	blood:	n/a	chr12:51566920-51566929 chr12:51566877-51566886 chr12:51566918-51566927
20	MAX	chr12:51566367-51567346	K562	blood:	n/a	chr12:51566637-51566647
21	ZBTB7A	chr12:51567116-51567269	K562	blood:	n/a	n/a
22	EP300	chr12:51566179-51567252	GM12878	blood:	n/a	chr12:51566704-51566711 chr12:51566584-51566600
23	POLR2A	chr12:51565728-51567300	HepG2	liver:	n/a	n/a
24	JUND	chr12:51565766-51567260	K562	blood:	n/a	chr12:51566919-51566928
25	POLR2A	chr12:51566300-51567332	Gliobla	brain:	n/a	n/a
26	PML	chr12:51566118-51567356	K562	blood:	n/a	n/a
27	POLR2A	chr12:51566074-51567303	GM12892	blood:	n/a	n/a
28	REST	chr12:51566735-51567299	PANC-1	pancreas:	n/a	n/a
29	MAX	chr12:51565910-51567384	K562	blood:	n/a	chr12:51566637-51566647
30	JUND	chr12:51566399-51567233	A549	lung:	n/a	chr12:51566919-51566928
31	MYC	chr12:51566085-51567327	K562	blood:	n/a	chr12:51566637-51566647
32	NFYA	chr12:51566464-51567233	Hela-S3	cervix:	n/a	chr12:51566875-51566890 chr12:51566875-51566890
33	TCF12	chr12:51566288-51567317	ECC-1	luminal epithelium:	n/a	n/a
34	TAF1	chr12:51566245-51567310	K562	blood:	n/a	n/a
35	POLR2A	chr12:51566119-51567297	GM15510	blood:	n/a	n/a
36	SP1	chr12:51566440-51567318	K562	blood:	n/a	chr12:51566615-51566624 chr12:51566614-51566623 chr12:51566614-51566628 chr12:51566613-51566625 chr12:51566637-51566651 chr12:51566619-51566626 chr12:51566613-51566625
37	BACH1	chr12:51567085-51567257	K562	blood:	n/a	n/a
38	WRNIP1	chr12:51565741-51567314	GM12878	blood:	n/a	n/a
39	POLR2A	chr12:51565945-51567317	Hela-S3	cervix:	n/a	n/a
40	USF1	chr12:51566587-51567244	A549	lung:	n/a	n/a
41	NRF1	chr12:51566761-51567323	GM12878	blood:	n/a	n/a
42	TBP	chr12:51566104-51567272	H1-hESC	embryonic stem cell:	n/a	n/a
43	MAZ	chr12:51565517-51567354	IMR90	lung:	n/a	chr12:51566637-51566647
44	SIN3A	chr12:51565933-51567270	H1-hESC	embryonic stem cell:	n/a	n/a
45	E2F6	chr12:51566198-51567276	K562	blood:	n/a	chr12:51566920-51566929 chr12:51566877-51566886 chr12:51566918-51566927 chr12:51566247-51566254
46	HDAC2	chr12:51566417-51567247	HepG2	liver:	n/a	chr12:51566813-51566821
47	TAF7	chr12:51566290-51567352	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr12:51566256-51567246	A549	lung:	n/a	n/a
49	HCFC1	chr12:51565477-51567445	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr12:51566071-51567261	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:51474365..51478814-chr12:51563597..51568148,9	K562	blood:
2	chr12:50793053..50795901-chr12:51566225..51568182,2	K562	blood:
3	chr12:51554796..51557300-chr12:51565911..51568570,2	K562	blood:
4	chr1:92931060..92931814-chr12:51567114..51568094,2	NB4	blood:
5	chr12:51564447..51569582-chr12:51630930..51635335,8	K562	blood:
6	chr12:51475324..51477948-chr12:51566462..51569488,3	MCF-7	breast:
7	chr12:51563450..51568971-chr12:51609008..51613972,14	K562	blood:
8	chr12:51565300..51568760-chr12:51661642..51664290,3	K562	blood:
9	chr12:51565491..51567919-chr12:51611128..51615638,5	K562	blood:
10	chr12:51440439..51443022-chr12:51565659..51567306,3	K562	blood:
11	chr12:51567118..51569511-chr12:51775066..51777946,2	K562	blood:
12	chr12:51474365..51480004-chr12:51564069..51568503,12	K562	blood:
13	chr12:51564257..51569582-chr12:51630930..51636873,13	K562	blood:

Variant related genes	Relation type
TFCP2	TF binding region
ENSG00000161813	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000139629	Chromatin interaction
ENSG00000170545	Chromatin interaction
ENSG00000199824	Chromatin interaction
ENSG00000184271	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10783414	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10783416	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10783417	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10783418	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10876143	0.85[EUR][1000 genomes]
rs10876146	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1565721	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1984544	0.81[ASN][1000 genomes]
rs2029686	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2436645	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2436646	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2436647	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2640511	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2640521	0.83[EUR][1000 genomes]
rs2640523	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2640527	0.81[ASN][1000 genomes]
rs2730647	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2730650	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2730654	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2956428	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6580799	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580800	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580801	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6580803	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6580804	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7306522	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51564800-51567400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:51564800-51567400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:51564800-51567400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr12:51564800-51567400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr12:51564800-51567400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:51564800-51567400	Active TSS	HMEC	breast
7	chr12:51565000-51567400	Active TSS	H1 Cell Line	embryonic stem cell
8	chr12:51565000-51567400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:51565000-51567400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:51565000-51567400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:51565000-51567400	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr12:51565000-51567400	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr12:51565000-51567400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:51565000-51567400	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr12:51565000-51567400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:51565000-51567400	Active TSS	NHLF	lung
17	chr12:51565000-51567800	Active TSS	K562	blood
18	chr12:51565200-51567400	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr12:51565200-51567400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:51565200-51567400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:51565200-51567400	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr12:51565200-51567400	Active TSS	GM12878-XiMat	blood
23	chr12:51565200-51567400	Active TSS	HSMM	muscle
24	chr12:51565200-51568600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:51565400-51567400	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr12:51565400-51567400	Active TSS	H9 Cell Line	embryonic stem cell
27	chr12:51565400-51567400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:51565400-51567400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:51565400-51567400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:51565400-51567400	Active TSS	Ovary	ovary
31	chr12:51565400-51567400	Active TSS	Psoas Muscle	Psoas
32	chr12:51565400-51567400	Active TSS	Stomach Mucosa	stomach
33	chr12:51565400-51567600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:51565400-51567600	Active TSS	Fetal Brain Female	brain
35	chr12:51565600-51567400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:51565600-51567400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:51565600-51567400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:51565600-51567400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:51565600-51567400	Active TSS	Aorta	Aorta
40	chr12:51565600-51567400	Active TSS	Fetal Kidney	kidney
41	chr12:51565600-51567400	Active TSS	Left Ventricle	heart
42	chr12:51565600-51567400	Active TSS	Lung	lung
43	chr12:51565600-51567400	Active TSS	Placenta Amnion	Placenta Amnion
44	chr12:51565600-51567400	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr12:51565600-51567400	Active TSS	Small Intestine	intestine
46	chr12:51565600-51567600	Active TSS	Colonic Mucosa	Colon
47	chr12:51565600-51567800	Active TSS	Placenta	Placenta
48	chr12:51565800-51567400	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr12:51565800-51567400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:51565800-51567400	Active TSS	Brain Angular Gyrus	brain

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