Variant report

Variant	rs12816228
Chromosome Location	chr12:24984295-24984296
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	FOS	chr12:24984242-24984424	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:24982376-24989601	K562	blood:	n/a	n/a
3	FOS	chr12:24984174-24984417	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr12:24984208-24987357	K562	blood:	n/a	n/a

Variant related genes	Relation type
BCAT1	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10047590	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10743524	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10842418	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11047661	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11047662	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11047664	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11047665	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11047666	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11047671	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11047673	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11047674	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11047679	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12372519	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17314214	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2046525	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34835991	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36035411	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4296116	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4432099	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4462438	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4603392	0.81[AMR][1000 genomes]
rs4963594	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4963807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4963815	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6487436	0.81[AMR][1000 genomes]
rs71450458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7965655	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7978793	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 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	nsv1053309	chr12:24770995-25078227	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer 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	11 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv1045302	chr12:24921100-25078227	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS 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	7 gene(s)	inside rSNPs	diseases
17	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
18	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
19	nsv1054863	chr12:24941350-25078227	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
20	nsv541426	chr12:24941350-25078227	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
21	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
22	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
23	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
24	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
25	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

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:24964000-25013400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:24965200-24989800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:24965600-24986800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:24965600-24989400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:24965600-25004800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:24965800-24989800	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:24966200-24987800	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:24966200-24989600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:24966200-25002000	Weak transcription	HepG2	liver
10	chr12:24967000-24989600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:24967800-24989000	Weak transcription	Aorta	Aorta
12	chr12:24968000-24990800	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:24968000-25017600	Weak transcription	Fetal Thymus	thymus
14	chr12:24968200-24985000	Weak transcription	Fetal Lung	lung
15	chr12:24968200-24986800	Weak transcription	Thymus	Thymus
16	chr12:24968400-25007800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr12:24969000-24991000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:24969200-25002200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:24969600-24989200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:24970000-24986400	Strong transcription	HUVEC	blood vessel
21	chr12:24970400-24985400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:24971000-25054800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:24971400-24995600	Weak transcription	Brain Angular Gyrus	brain
24	chr12:24972000-24990800	Weak transcription	Fetal Stomach	stomach
25	chr12:24972000-25004200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:24972400-24990800	Weak transcription	Placenta	Placenta
27	chr12:24972800-24987000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:24973400-24991400	Weak transcription	Fetal Brain Male	brain
29	chr12:24974400-25001800	Weak transcription	Pancreas	Pancrea
30	chr12:24975000-24989200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:24975000-24992200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:24975400-24989400	Weak transcription	Ovary	ovary
33	chr12:24975600-24992000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:24975600-24993200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:24975800-24990800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr12:24976400-24993400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:24977000-24985000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:24977000-24989000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:24978000-24984600	Weak transcription	GM12878-XiMat	blood
40	chr12:24978200-24987800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:24978600-24989800	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr12:24979200-24985000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:24979200-25007000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:24980400-24984400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
45	chr12:24981200-24984400	Weak transcription	Osteobl	bone
46	chr12:24981200-24990800	Weak transcription	Brain Anterior Caudate	brain
47	chr12:24981400-24984400	Weak transcription	NH-A	brain
48	chr12:24981400-24985200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr12:24981600-24985000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:24981800-24984800	Weak transcription	HSMMtube	muscle

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