Variant report

Variant	rs12230643
Chromosome Location	chr12:46949205-46949206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46765672..46767506-chr12:46948765..46951182,2	MCF-7	breast:
2	chr12:46941171..46945201-chr12:46945236..46949422,7	K562	blood:
3	chr12:46748960..46751313-chr12:46947807..46949856,2	MCF-7	breast:
4	chr12:46942932..46945589-chr12:46948248..46950851,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134294	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10492250	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11183544	0.82[ASN][1000 genomes]
rs73103305	0.89[EUR][1000 genomes];0.94[ASN][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	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases
5	esv3402095	chr12:46937340-46983181	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46940200-46950400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:46940200-46955000	Enhancers	HMEC	breast
3	chr12:46940600-46953600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:46941400-46956200	Weak transcription	Primary B cells from cord blood	blood
5	chr12:46942800-46949400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:46944200-46949400	Enhancers	Hela-S3	cervix
7	chr12:46944200-46949600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:46946400-46949400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr12:46946400-46949400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:46946400-46949400	Enhancers	NHLF	lung
11	chr12:46946600-46949600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:46946600-46949600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:46947000-46949400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr12:46947000-46949400	Enhancers	HSMM	muscle
15	chr12:46947000-46949400	Enhancers	HSMMtube	muscle
16	chr12:46947000-46950000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr12:46947200-46950000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr12:46947200-46956000	Weak transcription	Left Ventricle	heart
19	chr12:46947400-46949600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:46947400-46949600	Enhancers	A549	lung
21	chr12:46947400-46949800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:46947600-46949400	Enhancers	NHDF-Ad	bronchial
23	chr12:46948200-46952400	Enhancers	Adipose Nuclei	Adipose
24	chr12:46948400-46949400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:46948400-46949400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:46948400-46950200	Enhancers	Fetal Kidney	kidney
27	chr12:46948600-46949400	Enhancers	Fetal Heart	heart
28	chr12:46948600-46950600	Enhancers	Rectal Smooth Muscle	rectum
29	chr12:46948600-46954200	Enhancers	Colon Smooth Muscle	Colon
30	chr12:46948800-46949400	Enhancers	Ovary	ovary
31	chr12:46948800-46949400	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr12:46948800-46949400	Enhancers	Stomach Smooth Muscle	stomach
33	chr12:46948800-46949400	Enhancers	NH-A	brain
34	chr12:46948800-46949800	Enhancers	Fetal Muscle Leg	muscle
35	chr12:46948800-46949800	Enhancers	Psoas Muscle	Psoas
36	chr12:46948800-46950000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:46948800-46950000	Enhancers	Fetal Intestine Large	intestine
38	chr12:46948800-46950200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr12:46948800-46950400	Enhancers	Fetal Stomach	stomach
40	chr12:46949000-46949400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:46949000-46949600	Enhancers	NHEK	skin
42	chr12:46949000-46954000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:46949000-46954000	Weak transcription	Aorta	Aorta
44	chr12:46949200-46949600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:46949200-46949800	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr12:46949200-46949800	Flanking Active TSS	Fetal Lung	lung
47	chr12:46949200-46950000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:46949200-46950000	Flanking Active TSS	Osteobl	bone
49	chr12:46949200-46950200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:46949200-46950200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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