Variant report

Variant	rs60258688
Chromosome Location	chr12:47074553-47074554
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46764550..46767963-chr12:47070058..47075038,6	MCF-7	breast:
2	chr12:46761001..46762516-chr12:47074349..47075888,2	K562	blood:
3	chr12:46760106..46768771-chr12:47062317..47074742,23	MCF-7	breast:
4	chr12:47074270..47075808-chr12:47077694..47079248,2	K562	blood:
5	chr12:46774047..46784224-chr12:47066154..47074786,21	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257261	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000257496	Chromatin interaction
ENSG00000258096	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11183535	1.00[AMR][1000 genomes]
rs11183558	1.00[AMR][1000 genomes]
rs11504525	1.00[AMR][1000 genomes]
rs11504526	1.00[AMR][1000 genomes]
rs12297833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12298909	1.00[AMR][1000 genomes]
rs12304575	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12304806	1.00[AMR][1000 genomes]
rs12304865	1.00[AMR][1000 genomes]
rs12305342	1.00[AMR][1000 genomes]
rs12305992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12307390	1.00[AMR][1000 genomes]
rs12315001	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12316510	1.00[AMR][1000 genomes]
rs12317112	1.00[AMR][1000 genomes]
rs12318411	1.00[AMR][1000 genomes]
rs12319423	1.00[AMR][1000 genomes]
rs12320033	1.00[AMR][1000 genomes]
rs73282116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73293966	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73293979	1.00[AFR][1000 genomes];1.00[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	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv3416674	chr12:46988689-47178369	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv558783	chr12:46996632-47144856	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47059600-47076800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:47059800-47076600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:47065200-47076200	Weak transcription	Psoas Muscle	Psoas
4	chr12:47070000-47077400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:47071000-47080600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:47071200-47074800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr12:47071800-47077400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:47072000-47076000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:47073600-47075000	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr12:47073800-47074600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr12:47073800-47074800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr12:47073800-47074800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr12:47073800-47074800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:47073800-47074800	Enhancers	HMEC	breast
15	chr12:47074000-47074600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:47074000-47074800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr12:47074000-47074800	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr12:47074000-47074800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr12:47074000-47074800	Enhancers	HSMM	muscle
20	chr12:47074000-47074800	Enhancers	NHEK	skin
21	chr12:47074200-47074600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:47074200-47076000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:47074400-47074600	Enhancers	H1 Cell Line	embryonic stem cell
24	chr12:47074400-47074600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:47074400-47074800	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr12:47074400-47074800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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