Variant report

Variant	rs60543890
Chromosome Location	chr12:123518187-123518188
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123507054..123512479-chr12:123514635..123518784,6	K562	blood:
2	chr12:123516372..123518949-chr12:123560194..123562309,2	MCF-7	breast:
3	chr12:123494454..123496444-chr12:123516463..123519162,2	K562	blood:

Variant related genes	Relation type
ENSG00000265526	Chromatin interaction
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs57143069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57190557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57530745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58251569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58283587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58463629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58570201	1.00[AMR][1000 genomes]
rs59107122	1.00[AMR][1000 genomes]
rs59312127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60052793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60442043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60726563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60817665	0.85[AFR][1000 genomes]
rs61685353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408811	1.00[AMR][1000 genomes]
rs73408817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73408898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411044	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73417309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73417352	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS 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	47 gene(s)	inside rSNPs	diseases
3	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
8	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv560494	chr12:123478378-123560731	Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123470400-123526600	Weak transcription	Fetal Lung	lung
2	chr12:123490200-123528200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:123491600-123526400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:123492000-123518600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr12:123496000-123526400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:123497400-123528600	Weak transcription	Ovary	ovary
7	chr12:123497800-123526000	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:123502200-123519200	Weak transcription	HSMMtube	muscle
9	chr12:123504200-123519000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:123504200-123528000	Weak transcription	HMEC	breast
11	chr12:123504400-123540200	Weak transcription	Hela-S3	cervix
12	chr12:123507400-123526000	Genic enhancers	Fetal Thymus	thymus
13	chr12:123509800-123518600	Weak transcription	NHDF-Ad	bronchial
14	chr12:123509800-123519000	Weak transcription	A549	lung
15	chr12:123509800-123519200	Weak transcription	HSMM	muscle
16	chr12:123509800-123519200	Weak transcription	Osteobl	bone
17	chr12:123509800-123525600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:123509800-123530400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:123510000-123518200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:123510000-123518600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr12:123510200-123519600	Strong transcription	Stomach Smooth Muscle	stomach
22	chr12:123510800-123519200	Strong transcription	Liver	Liver
23	chr12:123511000-123519400	Strong transcription	Fetal Stomach	stomach
24	chr12:123511400-123528200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:123512800-123518800	Strong transcription	Brain Germinal Matrix	brain
26	chr12:123513600-123518200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:123514200-123519400	Strong transcription	Fetal Brain Female	brain
28	chr12:123514800-123518200	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:123515200-123519000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:123515400-123518600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:123515400-123519200	Strong transcription	Fetal Intestine Small	intestine
32	chr12:123515600-123519200	Strong transcription	NHLF	lung
33	chr12:123515600-123521600	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr12:123515800-123518600	Weak transcription	Psoas Muscle	Psoas
35	chr12:123516000-123518800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:123516000-123518800	Strong transcription	Adipose Nuclei	Adipose
37	chr12:123516000-123518800	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:123516000-123519000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:123516000-123519000	Strong transcription	Fetal Intestine Large	intestine
40	chr12:123516000-123519400	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr12:123516200-123519000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr12:123516400-123518400	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr12:123516400-123519000	Strong transcription	Colonic Mucosa	Colon
44	chr12:123516400-123519200	Strong transcription	Right Ventricle	heart
45	chr12:123516400-123527400	Weak transcription	Brain Hippocampus Middle	brain
46	chr12:123516600-123518400	Strong transcription	Aorta	Aorta
47	chr12:123516600-123519400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:123516600-123527800	Weak transcription	Stomach Mucosa	stomach
49	chr12:123516800-123519400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:123517000-123518200	Weak transcription	Primary B cells from cord blood	blood

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