Variant report

Variant	rs6489249
Chromosome Location	chr12:123527906-123527907
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123527734..123528656-chr12:123722305..123723382,7	MCF-7	breast:
2	chr12:123521446..123523784-chr12:123527111..123528952,2	K562	blood:
3	chr12:123527736..123529546-chr12:123540101..123542162,2	K562	blood:
4	chr12:123527749..123528657-chr12:123633701..123634611,3	MCF-7	breast:
5	chr12:123527755..123528597-chr12:123722388..123723377,4	MCF-7	breast:
6	chr12:123527304..123529634-chr12:123630952..123633326,2	MCF-7	breast:
7	chr12:123527678..123528658-chr12:123634881..123635709,3	MCF-7	breast:
8	chr12:123525729..123528577-chr12:123717047..123721067,3	MCF-7	breast:
9	chr12:123527596..123531182-chr12:123539339..123542162,4	K562	blood:
10	chr12:123519670..123521878-chr12:123527130..123529862,2	MCF-7	breast:
11	chr12:123527678..123528374-chr12:123635168..123636082,3	MCF-7	breast:
12	chr12:123525430..123528340-chr12:123721388..123723225,2	MCF-7	breast:
13	chr12:123459431..123461941-chr12:123526228..123528225,2	MCF-7	breast:
14	chr12:123521317..123522867-chr12:123526322..123528155,2	MCF-7	breast:
15	chr12:123526656..123529148-chr12:123634939..123636869,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000130921	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000111325	Chromatin interaction
ENSG00000090975	Chromatin interaction
ENSG00000256028	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10848426	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11060881	1.00[MEX][hapmap]
rs11060946	0.92[ASW][hapmap]
rs12312372	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12318362	0.92[AFR][1000 genomes]
rs4080877	1.00[MEX][hapmap]
rs6489252	0.92[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs7132517	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7302976	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7313800	0.82[AFR][1000 genomes]
rs7966050	0.92[ASW][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap]

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6489249	ABCB9	cis	lymphoblastoid	seeQTL
rs6489249	GPR109B	cis	lymphoblastoid	seeQTL
rs6489249	VPS37B	cis	lymphoblastoid	seeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123490200-123528200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr12:123497400-123528600	Weak transcription	Ovary	ovary
3	chr12:123504200-123528000	Weak transcription	HMEC	breast
4	chr12:123504400-123540200	Weak transcription	Hela-S3	cervix
5	chr12:123509800-123530400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:123511400-123528200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:123518200-123528000	Weak transcription	Brain Anterior Caudate	brain
8	chr12:123518200-123535600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:123518400-123533600	Weak transcription	Aorta	Aorta
10	chr12:123518800-123528200	Weak transcription	Brain Substantia Nigra	brain
11	chr12:123518800-123540600	Weak transcription	HepG2	liver
12	chr12:123519000-123528200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:123519000-123528200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:123519000-123540400	Weak transcription	Gastric	stomach
15	chr12:123519000-123543400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:123519400-123528200	Weak transcription	Brain Angular Gyrus	brain
17	chr12:123519400-123528200	Weak transcription	Fetal Brain Female	brain
18	chr12:123519600-123528200	Weak transcription	HSMMtube	muscle
19	chr12:123519800-123528000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr12:123521600-123528000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr12:123524400-123528000	Weak transcription	Adipose Nuclei	Adipose
22	chr12:123525000-123528200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr12:123525200-123528200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:123525400-123528200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:123525400-123528400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:123525400-123529400	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr12:123525400-123530000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:123526000-123529800	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
29	chr12:123526000-123531000	Enhancers	Placenta	Placenta
30	chr12:123526000-123531400	Enhancers	Colon Smooth Muscle	Colon
31	chr12:123526400-123528200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:123526400-123529000	Enhancers	Fetal Muscle Trunk	muscle
33	chr12:123526400-123529200	Enhancers	NHLF	lung
34	chr12:123526400-123530400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr12:123526400-123530800	Enhancers	Fetal Muscle Leg	muscle
36	chr12:123526400-123531000	Enhancers	Brain Cingulate Gyrus	brain
37	chr12:123526400-123531000	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr12:123526400-123531600	Enhancers	Rectal Smooth Muscle	rectum
39	chr12:123526600-123528000	Weak transcription	Pancreas	Pancrea
40	chr12:123526600-123528400	Enhancers	Fetal Lung	lung
41	chr12:123526600-123528800	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr12:123526600-123528800	Enhancers	Fetal Intestine Large	intestine
43	chr12:123526600-123530800	Enhancers	Left Ventricle	heart
44	chr12:123526600-123531200	Enhancers	Right Atrium	heart
45	chr12:123526800-123528000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr12:123526800-123528200	Weak transcription	Esophagus	oesophagus
47	chr12:123526800-123528200	Weak transcription	Lung	lung
48	chr12:123526800-123530600	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr12:123526800-123531200	Enhancers	Fetal Heart	heart
50	chr12:123527200-123528200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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