Variant report

Variant	rs60894374
Chromosome Location	chr12:123578619-123578620
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123575749..123580270-chr12:123716627..123719532,4	MCF-7	breast:
2	chr12:123576872..123579106-chr12:123620146..123621821,2	K562	blood:
3	chr12:123552557..123554332-chr12:123575460..123578722,3	MCF-7	breast:
4	chr12:123569324..123574207-chr12:123574392..123579398,5	K562	blood:
5	chr12:123577637..123579510-chr12:123716149..123718787,2	MCF-7	breast:
6	chr12:123459532..123461382-chr12:123578582..123581512,2	MCF-7	breast:

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

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs4427600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
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]
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]
rs7964036	0.82[AFR][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	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	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

No data

Chromatin state (count:90 , 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	chr12:123562400-123586600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr12:123567400-123588000	Enhancers	Left Ventricle	heart
6	chr12:123569200-123578800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:123569200-123579400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:123569800-123579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:123570000-123579800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr12:123570600-123578800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:123570800-123580200	Enhancers	HMEC	breast
12	chr12:123570800-123586600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:123571000-123586600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr12:123571200-123600000	Genic enhancers	Thymus	Thymus
15	chr12:123571400-123578800	Weak transcription	Brain Anterior Caudate	brain
16	chr12:123571400-123580000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr12:123571800-123582200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:123573200-123584200	Enhancers	Liver	Liver
19	chr12:123574000-123579000	Enhancers	HepG2	liver
20	chr12:123574400-123579000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:123574400-123579200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:123574400-123586800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:123574800-123579000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:123575600-123579200	Weak transcription	HUVEC	blood vessel
25	chr12:123576200-123579200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:123576400-123589400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:123576600-123579400	Weak transcription	Primary T cells from cord blood	blood
28	chr12:123576600-123581400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:123576600-123588600	Enhancers	Right Ventricle	heart
30	chr12:123576800-123583200	Weak transcription	Primary B cells from cord blood	blood
31	chr12:123577000-123579000	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr12:123577000-123580200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:123577000-123581000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:123577000-123590400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr12:123577200-123581200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:123577200-123584400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:123577200-123586800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:123577400-123582400	Enhancers	Fetal Heart	heart
39	chr12:123577400-123589600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:123577400-123590200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr12:123577800-123579200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:123577800-123579200	Weak transcription	NHEK	skin
43	chr12:123577800-123579800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:123577800-123581400	Enhancers	Psoas Muscle	Psoas
45	chr12:123578000-123579000	Enhancers	Hela-S3	cervix
46	chr12:123578000-123580200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:123578000-123580800	Enhancers	Lung	lung
48	chr12:123578000-123580800	Enhancers	Ovary	ovary
49	chr12:123578000-123581200	Enhancers	Esophagus	oesophagus
50	chr12:123578000-123581400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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