Variant report

Variant	rs2242399
Chromosome Location	chr12:25097606-25097607
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	CEBPB	chr12:25097538-25098295	K562	blood:	n/a	chr12:25097690-25097701 chr12:25097895-25097906 chr12:25097701-25097712 chr12:25098187-25098199
2	POLR2A	chr12:25086081-25102562	K562	blood:	n/a	n/a
3	CEBPB	chr12:25097514-25097863	IMR90	lung:	n/a	chr12:25097690-25097701 chr12:25097701-25097712
4	CEBPB	chr12:25097566-25097800	A549	lung:	n/a	chr12:25097690-25097701 chr12:25097701-25097712
5	POLR2A	chr12:25096779-25098450	H1-hESC	embryonic stem cell:	n/a	n/a
6	CEBPB	chr12:25097593-25097781	H1-hESC	embryonic stem cell:	n/a	chr12:25097690-25097701 chr12:25097701-25097712
7	MXI1	chr12:25096833-25097643	IMR90	lung:	n/a	n/a
8	CEBPB	chr12:25097554-25098280	HepG2	liver:	n/a	chr12:25097690-25097701 chr12:25097895-25097906 chr12:25097701-25097712 chr12:25098187-25098199
9	POLR2A	chr12:25096841-25097611	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:25096555..25099417-chr12:25125856..25128677,2	K562	blood:

Variant related genes	Relation type
ENSG00000255921	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1032589	0.89[YRI][hapmap]
rs10842439	0.89[YRI][hapmap]
rs11047721	1.00[YRI][hapmap]
rs1875091	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422312	chr12:24519392-25221686	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv898920	chr12:24648863-25147192	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1041221	chr12:24880443-25213168	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv541425	chr12:24880443-25213168	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active 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 miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv469170	chr12:24891175-25204353	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv557776	chr12:24891175-25204353	Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv557777	chr12:24891175-25205241	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv469173	chr12:24891175-25207653	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv557778	chr12:24891175-25207653	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv1049138	chr12:24921100-25164524	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
16	nsv1051319	chr12:24921100-25238936	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
17	nsv1051968	chr12:24941350-25138118	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
18	nsv541427	chr12:24941350-25138118	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
19	nsv1037288	chr12:24941350-25238936	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
20	nsv541428	chr12:24941350-25238936	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
21	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
22	nsv832353	chr12:25060820-25119975	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
23	esv3378403	chr12:25084023-25181017	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25083600-25098200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:25083600-25098600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:25084200-25098600	Weak transcription	Fetal Thymus	thymus
4	chr12:25084800-25099800	Weak transcription	Thymus	Thymus
5	chr12:25086800-25100000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:25089800-25098600	Weak transcription	Ovary	ovary
7	chr12:25091200-25098200	Weak transcription	NHLF	lung
8	chr12:25091400-25098400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:25091400-25098600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:25091400-25099000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:25091400-25099400	Weak transcription	NHEK	skin
12	chr12:25091600-25098600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:25091600-25101000	Weak transcription	Lung	lung
14	chr12:25091800-25099600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:25092000-25099600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:25092800-25101400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:25093200-25098400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr12:25093800-25100400	Weak transcription	Fetal Stomach	stomach
19	chr12:25094800-25099200	Weak transcription	Primary T cells from cord blood	blood
20	chr12:25095000-25099600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr12:25096200-25098600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:25096200-25098800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:25096400-25098200	Weak transcription	Fetal Muscle Leg	muscle
24	chr12:25096400-25098200	Weak transcription	Pancreas	Pancrea
25	chr12:25096800-25098600	Genic enhancers	HUES64 Cell Line	embryonic stem cell
26	chr12:25096800-25098600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr12:25097000-25098200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:25097000-25098200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:25097000-25098400	Genic enhancers	H1 Cell Line	embryonic stem cell
30	chr12:25097000-25098400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
31	chr12:25097000-25098400	Genic enhancers	Primary hematopoietic stem cells	blood
32	chr12:25097000-25098400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:25097000-25098400	Enhancers	Muscle Satellite Cultured Cells	--
34	chr12:25097000-25098400	Transcr. at gene 5' and 3'	K562	blood
35	chr12:25097000-25098400	Genic enhancers	NH-A	brain
36	chr12:25097000-25098600	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr12:25097000-25098600	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr12:25097000-25098600	Genic enhancers	Dnd41	blood
39	chr12:25097000-25098800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:25097000-25099000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
41	chr12:25097000-25099800	Enhancers	HepG2	liver
42	chr12:25097000-25100000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr12:25097000-25100600	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr12:25097200-25098000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:25097200-25098600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:25097200-25098800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:25097200-25099000	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr12:25097400-25097800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:25097400-25098000	Enhancers	HSMM	muscle
50	chr12:25097400-25098400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood

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