Variant report

Variant	rs12424725
Chromosome Location	chr12:75945797-75945798
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75936274..75938020-chr12:75944642..75947136,2	MCF-7	breast:
2	chr12:75942170..75945016-chr12:75945671..75947951,2	MCF-7	breast:
3	chr12:75904950..75907035-chr12:75944732..75947463,2	K562	blood:

Variant related genes	Relation type
ENSG00000111615	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1026783	0.80[ASN][1000 genomes]
rs12422473	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12423477	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12423509	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12424436	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12424441	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12425236	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12425465	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12578478	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12579390	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2279246	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34281469	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3782225	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58248634	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58391657	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv470305	chr12:75896688-75987360	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75938600-75947200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:75942800-75945800	Weak transcription	Fetal Brain Male	brain
3	chr12:75942800-75947400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:75942800-75947400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:75943000-75947200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:75943000-75947200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:75944400-75945800	Enhancers	Fetal Stomach	stomach
8	chr12:75944400-75947400	Weak transcription	A549	lung
9	chr12:75944400-75947600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:75944600-75946200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:75944600-75947200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:75944600-75947200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:75944600-75947200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:75944600-75947200	Weak transcription	NH-A	brain
15	chr12:75944800-75945800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:75944800-75947200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:75944800-75947400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:75944800-75948200	Weak transcription	Lung	lung
19	chr12:75944800-75948200	Weak transcription	Right Atrium	heart
20	chr12:75944800-75954000	Weak transcription	Pancreas	Pancrea
21	chr12:75945000-75947200	Weak transcription	NHDF-Ad	bronchial
22	chr12:75945000-75947400	Weak transcription	Adipose Nuclei	Adipose
23	chr12:75945000-75947400	Weak transcription	NHLF	lung
24	chr12:75945200-75946400	Weak transcription	Fetal Brain Female	brain
25	chr12:75945200-75947200	Weak transcription	Fetal Lung	lung
26	chr12:75945200-75947200	Weak transcription	Fetal Muscle Leg	muscle
27	chr12:75945200-75947400	Weak transcription	Fetal Kidney	kidney
28	chr12:75945400-75946000	Enhancers	Stomach Mucosa	stomach
29	chr12:75945400-75947200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:75945400-75947400	Weak transcription	HSMM	muscle
31	chr12:75945400-75948800	Enhancers	Fetal Heart	heart
32	chr12:75945600-75945800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:75945600-75946200	Weak transcription	HSMMtube	muscle

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