Variant report

Variant	rs11047725
Chromosome Location	chr12:25104269-25104270
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	POLR2A	chr12:25099831-25105595	GM12892	blood:	n/a	n/a
2	RUNX3	chr12:25102748-25105659	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:25099474-25105917	GM12878	blood:	n/a	n/a
4	POU2F2	chr12:25103164-25104459	GM12878	blood:	n/a	chr12:25103391-25103404 chr12:25103391-25103404
5	ZNF384	chr12:25103828-25105684	K562	blood:	n/a	n/a
6	MTA3	chr12:25100193-25106014	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:25102982-25105203	GM12892	blood:	n/a	n/a
8	POLR2A	chr12:25100481-25105858	GM12878	blood:	n/a	n/a
9	NFIC	chr12:25102781-25105970	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:25103199-25105336	GM12878	blood:	n/a	n/a
11	SREBP1	chr12:25104260-25106173	GM12878	blood:	n/a	n/a
12	PML	chr12:25102911-25105884	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:25100657-25105244	GM12892	blood:	n/a	n/a
14	STAT5A	chr12:25104174-25105585	GM12878	blood:	n/a	n/a
15	POU2F2	chr12:25104231-25105123	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:25103272-25105488	GM18505	blood:	n/a	n/a
17	FOXM1	chr12:25103024-25104361	GM12878	blood:	n/a	n/a
18	STAT5A	chr12:25103310-25104313	GM12878	blood:	n/a	n/a
19	MTA3	chr12:25100433-25105538	GM12878	blood:	n/a	n/a
20	GATA1	chr12:25103051-25104275	K562	blood:	n/a	chr12:25103383-25103399 chr12:25103405-25103422 chr12:25103386-25103395
21	POLR2A	chr12:25099442-25105564	GM12878	blood:	n/a	n/a
22	NFATC1	chr12:25103160-25105394	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:25102967-25105197	GM12878	blood:	n/a	n/a
24	POLR2A	chr12:25100014-25105577	GM12892	blood:	n/a	n/a
25	POLR2A	chr12:25103855-25105270	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:25103196-25105221	GM12892	blood:	n/a	n/a
27	POLR2A	chr12:25104167-25104528	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:25102694..25105038-chr12:25299270..25301351,2	MCF-7	breast:
2	chr12:25069181..25071774-chr12:25102558..25104907,2	K562	blood:
3	chr12:25103176..25105758-chr12:25114864..25117821,2	K562	blood:

Variant related genes	Relation type
BCAT1	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1032589	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10743528	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10842435	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842438	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11047721	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11047734	0.86[AMR][1000 genomes]
rs1566405	0.84[AMR][1000 genomes]
rs1603552	0.86[AMR][1000 genomes]
rs1603553	0.86[AMR][1000 genomes]
rs2645909	0.86[AMR][1000 genomes]
rs2649764	0.86[AMR][1000 genomes]
rs2649765	0.86[AMR][1000 genomes]
rs2649766	0.81[AMR][1000 genomes]
rs2649767	0.84[AMR][1000 genomes]
rs2728656	0.86[AMR][1000 genomes]
rs4963836	0.86[AMR][1000 genomes]
rs6487446	0.86[AMR][1000 genomes]
rs7312807	0.81[EUR][1000 genomes]
rs7954046	0.80[EUR][1000 genomes]
rs7954135	0.80[EUR][1000 genomes]
rs7965671	0.95[ASN][1000 genomes]
rs7978200	0.86[AMR][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:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25101800-25106200	Flanking Active TSS	GM12878-XiMat	blood
2	chr12:25102400-25104600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:25102400-25104600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:25102400-25105400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:25102400-25105600	Enhancers	Placenta	Placenta
6	chr12:25102600-25104600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:25102600-25104600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr12:25102600-25104600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr12:25102600-25104600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:25102600-25104600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr12:25102600-25104800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:25102600-25104800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:25102600-25105200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:25102800-25104600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:25102800-25104600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr12:25102800-25104800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:25102800-25105800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr12:25103200-25104800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:25103400-25104800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:25103600-25104800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:25103800-25104600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:25103800-25104800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:25103800-25104800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:25103800-25104800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr12:25103800-25104800	Weak transcription	Fetal Heart	heart
26	chr12:25104000-25104400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:25104000-25104400	Weak transcription	HepG2	liver
28	chr12:25104000-25104600	Enhancers	K562	blood
29	chr12:25104000-25105200	Enhancers	Placenta Amnion	Placenta Amnion
30	chr12:25104200-25104400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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