Variant report

Variant	rs4427600
Chromosome Location	chr12:123574838-123574839
allele	A/G
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123573881..123576493-chr12:123631498..123633206,2	K562	blood:
2	chr12:123559026..123560660-chr12:123573031..123574900,2	MCF-7	breast:
3	chr12:123539791..123542781-chr12:123573369..123575868,2	MCF-7	breast:
4	chr12:123574271..123575945-chr12:123599295..123601794,2	MCF-7	breast:
5	chr12:123574636..123576162-chr12:123864283..123866660,2	K562	blood:
6	chr12:123574363..123577127-chr12:123716217..123719008,2	K562	blood:
7	chr12:123574363..123577127-chr12:123716097..123719008,3	K562	blood:
8	chr12:123561700..123563404-chr12:123573339..123575824,2	MCF-7	breast:
9	chr12:123569324..123574207-chr12:123574392..123579398,5	K562	blood:
10	chr12:123573280..123576168-chr12:123580609..123582204,2	K562	blood:
11	chr12:123463514..123465244-chr12:123572916..123575851,2	MCF-7	breast:
12	chr12:123468080..123470439-chr12:123573373..123575937,2	K562	blood:
13	chr12:123557772..123560593-chr12:123574740..123576717,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000090975	Chromatin interaction
ENSG00000182196	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11060999	0.83[ASW][hapmap]
rs12311043	0.83[ASW][hapmap];0.82[MKK][hapmap]
rs55820451	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55992397	0.80[AFR][1000 genomes]
rs56846082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57178349	0.82[AFR][1000 genomes]
rs58282663	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58490757	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59995499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60167440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60200203	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60235187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60320128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60424338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60546720	0.80[AFR][1000 genomes]
rs60894374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61089898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61110645	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61396549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411090	0.82[AFR][1000 genomes]
rs73411093	0.81[AFR][1000 genomes]
rs73413223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413226	0.82[AFR][1000 genomes]
rs73413228	0.82[AFR][1000 genomes]
rs73413230	0.82[AFR][1000 genomes]
rs73413241	0.82[AFR][1000 genomes]
rs73413246	0.82[AFR][1000 genomes]
rs752164	0.83[ASW][hapmap];0.81[LWK][hapmap];1.00[MKK][hapmap]
rs7952760	0.81[ASW][hapmap];0.81[LWK][hapmap];1.00[MKK][hapmap]
rs7964036	0.83[ASW][hapmap];0.81[LWK][hapmap];1.00[MKK][hapmap];0.82[AFR][1000 genomes]
rs7967118	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	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
6	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
7	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4427600	OGFOD2	cis	lymphoblastoid	seeQTL
rs4427600	ABCB9	cis	lymphoblastoid	seeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123561000-123578800	Weak transcription	Fetal Intestine Large	intestine
2	chr12:123561200-123590000	Weak transcription	Fetal Intestine Small	intestine
3	chr12:123561600-123604000	Genic enhancers	Fetal Thymus	thymus
4	chr12:123562000-123576200	Weak transcription	Primary T cells from cord blood	blood
5	chr12:123562400-123586600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:123567400-123588000	Enhancers	Left Ventricle	heart
7	chr12:123568600-123578000	Weak transcription	Colonic Mucosa	Colon
8	chr12:123568800-123576600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:123569200-123578800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:123569200-123579400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:123569800-123576200	Weak transcription	Ovary	ovary
12	chr12:123569800-123578200	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:123569800-123579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:123570000-123579800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr12:123570600-123578600	Weak transcription	Aorta	Aorta
16	chr12:123570600-123578600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:123570600-123578600	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:123570600-123578800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:123570800-123578200	Weak transcription	Stomach Mucosa	stomach
20	chr12:123570800-123578600	Weak transcription	Pancreas	Pancrea
21	chr12:123570800-123580200	Enhancers	HMEC	breast
22	chr12:123570800-123586600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:123571000-123575600	Weak transcription	Spleen	Spleen
24	chr12:123571000-123586600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr12:123571200-123600000	Genic enhancers	Thymus	Thymus
26	chr12:123571400-123578800	Weak transcription	Brain Anterior Caudate	brain
27	chr12:123571400-123580000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:123571600-123576400	Weak transcription	Lung	lung
29	chr12:123571600-123578000	Weak transcription	Esophagus	oesophagus
30	chr12:123571600-123578200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr12:123571600-123578200	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:123571600-123578600	Weak transcription	Brain Angular Gyrus	brain
33	chr12:123571800-123582200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr12:123572400-123575800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:123572600-123577400	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr12:123572800-123577200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:123573000-123577200	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr12:123573200-123575000	Enhancers	GM12878-XiMat	blood
39	chr12:123573200-123584200	Enhancers	Liver	Liver
40	chr12:123573400-123575000	Enhancers	HSMMtube	muscle
41	chr12:123573400-123575000	Enhancers	Osteobl	bone
42	chr12:123573400-123575400	Enhancers	NHDF-Ad	bronchial
43	chr12:123573400-123575400	Enhancers	NHLF	lung
44	chr12:123573400-123575600	Enhancers	Hela-S3	cervix
45	chr12:123573400-123575600	Enhancers	HUVEC	blood vessel
46	chr12:123573400-123576200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:123573400-123576400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr12:123573600-123575000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:123573800-123575000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:123573800-123575200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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