Variant report

Variant	rs12296616
Chromosome Location	chr12:9517045-9517046
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:162)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:162 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:9516546-9517515	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:9516729-9517905	GM12878	blood:	n/a	n/a
3	BATF	chr12:9516696-9517884	GM12878	blood:	n/a	n/a
4	MEF2A	chr12:9516791-9518262	GM12878	blood:	n/a	n/a
5	TBP	chr12:9516919-9518117	GM12878	blood:	n/a	n/a
6	MXI1	chr12:9516988-9517917	GM12878	blood:	n/a	n/a
7	POU2F2	chr12:9516664-9517787	GM12891	blood:	n/a	n/a
8	POLR2A	chr12:9516672-9518064	U87	brain:	n/a	n/a
9	BCL11A	chr12:9516825-9517859	GM12878	blood:	n/a	n/a
10	TBL1XR1	chr12:9515537-9518036	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:9516826-9517105	Gliobla	brain:	n/a	n/a
12	TBP	chr12:9516916-9517344	HepG2	liver:	n/a	n/a
13	HEY1	chr12:9516721-9517413	HepG2	liver:	n/a	n/a
14	SRF	chr12:9516956-9517842	GM12878	blood:	n/a	n/a
15	EP300	chr12:9516766-9517567	GM12878	blood:	n/a	n/a
16	MEF2C	chr12:9516773-9517829	GM12878	blood:	n/a	n/a
17	JUND	chr12:9516829-9518060	GM12878	blood:	n/a	chr12:9517603-9517614
18	MAX	chr12:9516965-9517905	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:9515357-9518289	GM12891	blood:	n/a	n/a
20	POLR2A	chr12:9516492-9517475	H1-hESC	embryonic stem cell:	n/a	n/a
21	RFX5	chr12:9516836-9517768	GM12878	blood:	n/a	n/a
22	MTA3	chr12:9513806-9518741	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:9516704-9517256	H1-hESC	embryonic stem cell:	n/a	n/a
24	CHD2	chr12:9516713-9518340	GM12878	blood:	n/a	n/a
25	NFIC	chr12:9516412-9518439	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:9515210-9518678	GM12892	blood:	n/a	n/a
27	RCOR1	chr12:9516850-9517788	GM12878	blood:	n/a	n/a
28	USF1	chr12:9516873-9517239	H1-hESC	embryonic stem cell:	n/a	n/a
29	TCF12	chr12:9516947-9517097	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr12:9516802-9517113	HepG2	liver:	n/a	n/a
31	PML	chr12:9516700-9517264	K562	blood:	n/a	n/a
32	PAX5	chr12:9516942-9517306	GM12878	blood:	n/a	n/a
33	TBP	chr12:9516899-9517302	K562	blood:	n/a	n/a
34	SP1	chr12:9516881-9517839	GM12878	blood:	n/a	n/a
35	PML	chr12:9516717-9517203	K562	blood:	n/a	n/a
36	POU2F2	chr12:9516681-9517838	GM12891	blood:	n/a	n/a
37	MAZ	chr12:9516915-9517907	GM12878	blood:	n/a	n/a
38	JUND	chr12:9517032-9517755	H1-hESC	embryonic stem cell:	n/a	chr12:9517603-9517614
39	SRF	chr12:9517030-9517176	GM12878	blood:	n/a	n/a
40	EBF1	chr12:9516711-9518338	GM12878	blood:	n/a	n/a
41	POLR2A	chr12:9516654-9517618	HL-60	blood:	n/a	n/a
42	POLR2A	chr12:9515459-9518442	GM12891	blood:	n/a	n/a
43	TBP	chr12:9516897-9517540	H1-hESC	embryonic stem cell:	n/a	n/a
44	HEY1	chr12:9516620-9517288	HepG2	liver:	n/a	n/a
45	ZBTB33	chr12:9516862-9517332	GM12878	blood:	n/a	n/a
46	POLR2A	chr12:9516943-9517147	MCF10A-Er-Src	breast:	n/a	n/a
47	ZNF143	chr12:9516943-9517534	H1-hESC	embryonic stem cell:	n/a	n/a
48	CREB1	chr12:9516804-9517992	GM12878	blood:	n/a	n/a
49	JUND	chr12:9516950-9517793	K562	blood:	n/a	chr12:9517603-9517614
50	POLR2A	chr12:9516640-9517971	GM12892	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:9514472..9517285-chr12:9517571..9520331,3	K562	blood:
2	chr12:9516871..9518767-chr12:9528942..9530878,2	MCF-7	breast:
3	chr12:9514676..9517481-chr12:9908794..9910668,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PZP-4	chr12:9516719-9517139	XLOC_010009

No data

Variant related genes	Relation type
ENSG00000260423	TF binding region
ENSG00000260423	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11050581	0.82[AMR][1000 genomes]
rs11050584	0.82[AMR][1000 genomes]
rs12311658	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv523958	chr12:9303440-9549072	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv557355	chr12:9309995-9529015	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1035953	chr12:9314481-9544655	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
6	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
7	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
8	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	nsv916832	chr12:9397450-9693952	ZNF genes & repeats Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv976736	chr12:9431362-9524845	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv898740	chr12:9436446-9546962	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1050161	chr12:9436635-9685768	Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv898741	chr12:9458525-9546962	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv1035958	chr12:9472365-9579109	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv898742	chr12:9473157-9518222	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv898743	chr12:9473157-9522350	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv975403	chr12:9481646-9541991	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	esv3436788	chr12:9499151-9519686	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	esv3332298	chr12:9500121-9519487	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	esv2760260	chr12:9504060-9519172	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9507000-9517200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:9514800-9517200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr12:9515000-9517800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr12:9515400-9517200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:9515400-9519200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:9515600-9518600	Enhancers	Primary B cells from peripheral blood	blood
7	chr12:9515800-9517200	Enhancers	K562	blood
8	chr12:9515800-9518200	Enhancers	HSMMtube	muscle
9	chr12:9515800-9518600	Enhancers	H9 Cell Line	embryonic stem cell
10	chr12:9515800-9520000	Enhancers	H1 Cell Line	embryonic stem cell
11	chr12:9515800-9520000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:9516000-9517200	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr12:9516000-9517200	Enhancers	HSMM	muscle
14	chr12:9516000-9518400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr12:9516000-9518400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:9516000-9519800	Weak transcription	Right Atrium	heart
17	chr12:9516000-9521200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:9516200-9518000	Enhancers	Brain Germinal Matrix	brain
19	chr12:9516400-9517200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr12:9516400-9518400	Enhancers	Brain Angular Gyrus	brain
21	chr12:9516400-9520000	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr12:9516600-9517200	Enhancers	NHEK	skin
23	chr12:9516600-9517400	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr12:9516600-9518000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:9516600-9518000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:9516600-9518400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:9516600-9520000	Enhancers	Fetal Stomach	stomach
28	chr12:9516800-9517200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:9516800-9517200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:9516800-9517200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:9516800-9517200	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr12:9516800-9517200	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr12:9516800-9517400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:9516800-9517400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:9516800-9517400	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr12:9516800-9517600	Enhancers	Fetal Muscle Trunk	muscle
37	chr12:9516800-9517600	Enhancers	Ovary	ovary
38	chr12:9516800-9517800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr12:9516800-9517800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:9516800-9518000	Flanking Active TSS	HepG2	liver
41	chr12:9516800-9518000	Flanking Active TSS	NH-A	brain
42	chr12:9516800-9518200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:9516800-9518400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:9516800-9518600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:9516800-9518600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:9516800-9520000	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr12:9516800-9520400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr12:9516800-9520600	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr12:9516800-9521600	Enhancers	Fetal Lung	lung
50	chr12:9517000-9517200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

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