Variant report

Variant	rs1946173
Chromosome Location	chr12:47065197-47065198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46760106..46768771-chr12:47062317..47074742,23	MCF-7	breast:
2	chr12:47060607..47062700-chr12:47063813..47065440,2	MCF-7	breast:
3	chr12:47061845..47064516-chr12:47065041..47068020,3	MCF-7	breast:
4	chr12:46885920..46888548-chr12:47063563..47066194,2	MCF-7	breast:
5	chr12:46763851..46768621-chr12:47062568..47068047,5	MCF-7	breast:
6	chr12:46659975..46662583-chr12:47064102..47065649,2	K562	blood:
7	chr12:47063637..47066439-chr12:47067771..47070292,2	K562	blood:

Variant related genes	Relation type
ENSG00000111371	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000258096	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11183557	1.00[AFR][1000 genomes]
rs12299524	0.85[AFR][1000 genomes]
rs12300875	0.85[AFR][1000 genomes]
rs12308056	1.00[AFR][1000 genomes]
rs12310253	0.81[AFR][1000 genomes]
rs12312764	0.98[AFR][1000 genomes]
rs12314549	0.92[AFR][1000 genomes]
rs12315703	1.00[AFR][1000 genomes]
rs12316011	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs12318292	0.81[AFR][1000 genomes]
rs12319714	0.81[AFR][1000 genomes]
rs12320094	0.85[AFR][1000 genomes]
rs235614	0.86[AFR][1000 genomes]
rs235615	0.86[AFR][1000 genomes]
rs235620	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs235623	0.80[YRI][hapmap]

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	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	esv1844378	chr12:47028797-47072016	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	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:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47046400-47069800	Weak transcription	Pancreas	Pancrea
2	chr12:47054000-47068400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:47054000-47071400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:47056000-47069000	Weak transcription	Esophagus	oesophagus
5	chr12:47059000-47065600	Weak transcription	Primary B cells from cord blood	blood
6	chr12:47059600-47069200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:47059600-47069800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr12:47059600-47076800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:47059800-47068800	Weak transcription	NHLF	lung
10	chr12:47059800-47076600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:47060000-47068000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:47060000-47068000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:47061400-47067600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:47061600-47067600	Weak transcription	NHEK	skin
15	chr12:47061600-47068000	Weak transcription	NHDF-Ad	bronchial
16	chr12:47062000-47067800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:47062200-47068000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:47062600-47068600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:47063600-47069800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:47063800-47065200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:47063800-47070800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr12:47064200-47065200	Enhancers	Psoas Muscle	Psoas
23	chr12:47064200-47071200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:47064400-47071000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:47064600-47070600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:47064600-47071200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:47064800-47065200	Enhancers	Left Ventricle	heart
28	chr12:47064800-47065200	Enhancers	Right Ventricle	heart
29	chr12:47064800-47065200	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr12:47064800-47067800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:47064800-47071200	Weak transcription	H9 Cell Line	embryonic stem cell

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