Variant report

Variant	rs61558457
Chromosome Location	chr12:48547117-48547118
allele	G/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	POLR2A	chr12:48546925-48547471	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:48546821-48547867	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:48546567-48547561	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:48547069-48547907	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr12:48546842-48547464	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr12:48547014-48547283	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:48547046-48547386	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48545842..48549323-chr12:48549562..48552963,3	MCF-7	breast:
2	chr12:48545367..48547255-chr12:48549317..48550994,3	MCF-7	breast:

Variant related genes	Relation type
ASB8	TF binding region
ENSG00000177981	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs55759881	0.83[AMR][1000 genomes]
rs55789595	0.83[AMR][1000 genomes]
rs55991805	1.00[AMR][1000 genomes]
rs57539024	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58148022	0.83[AMR][1000 genomes]
rs58373242	0.83[AMR][1000 genomes]
rs59051221	1.00[AMR][1000 genomes]
rs59233899	0.82[AFR][1000 genomes]
rs59643562	1.00[AMR][1000 genomes]
rs59787033	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59896935	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60001451	1.00[AMR][1000 genomes]
rs60316794	1.00[AMR][1000 genomes]
rs61750873	0.83[AMR][1000 genomes]
rs7316275	1.00[AMR][1000 genomes]
rs74086781	0.83[AMR][1000 genomes]
rs74086968	0.83[AMR][1000 genomes]
rs74086984	1.00[AMR][1000 genomes]
rs74089112	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089135	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74089149	1.00[AMR][1000 genomes]
rs74089151	1.00[AMR][1000 genomes]
rs74089154	1.00[AMR][1000 genomes]
rs74089161	1.00[AMR][1000 genomes]
rs74089171	1.00[AMR][1000 genomes]
rs74089540	0.83[AMR][1000 genomes]
rs74089548	0.83[AMR][1000 genomes]
rs74089549	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS 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	39 gene(s)	inside rSNPs	diseases
5	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48516200-48547200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:48516400-48547200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:48516400-48547200	Strong transcription	Stomach Smooth Muscle	stomach
4	chr12:48516400-48547800	Strong transcription	Fetal Stomach	stomach
5	chr12:48516800-48547400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:48517600-48547400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:48518600-48547600	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:48519600-48547200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr12:48520800-48547400	Strong transcription	Fetal Brain Female	brain
10	chr12:48523800-48547400	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:48526200-48547600	Strong transcription	Adipose Nuclei	Adipose
12	chr12:48530200-48547600	Strong transcription	Placenta	Placenta
13	chr12:48531000-48547400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:48531000-48547800	Strong transcription	Fetal Muscle Trunk	muscle
15	chr12:48531200-48547400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:48531200-48547400	Strong transcription	Duodenum Mucosa	Duodenum
17	chr12:48531200-48547400	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:48531200-48547400	Strong transcription	Fetal Intestine Large	intestine
19	chr12:48531200-48547600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:48531200-48547600	Strong transcription	HMEC	breast
21	chr12:48531200-48547800	Strong transcription	Primary T cells from cord blood	blood
22	chr12:48531200-48547800	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr12:48531200-48547800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr12:48531200-48548000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:48531400-48547400	Strong transcription	Colonic Mucosa	Colon
26	chr12:48531400-48548000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:48531600-48547200	Strong transcription	Brain Hippocampus Middle	brain
28	chr12:48531600-48547400	Strong transcription	Lung	lung
29	chr12:48531600-48547800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:48532200-48548400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr12:48533000-48547400	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:48533000-48547800	Strong transcription	Liver	Liver
33	chr12:48533200-48547600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:48533200-48547800	Strong transcription	Fetal Thymus	thymus
35	chr12:48533600-48547400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:48533600-48548400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr12:48533800-48547800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr12:48534200-48547400	Strong transcription	Brain Cingulate Gyrus	brain
39	chr12:48534200-48548000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr12:48534400-48547600	Strong transcription	Dnd41	blood
41	chr12:48535000-48547800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:48535800-48547400	Strong transcription	Primary B cells from cord blood	blood
43	chr12:48536200-48547400	Strong transcription	Osteobl	bone
44	chr12:48536400-48548200	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr12:48536600-48547800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:48536800-48550800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr12:48537800-48550600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr12:48538400-48550200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:48538600-48548600	Strong transcription	Thymus	Thymus
50	chr12:48539200-48547800	Strong transcription	Rectal Smooth Muscle	rectum

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