Variant report

Variant	rs12993270
Chromosome Location	chr2:62723474-62723475
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:62722458..62725305-chr2:62733715..62736301,2	MCF-7	breast:
2	chr2:62723131..62724977-chr2:62729168..62731291,2	K562	blood:
3	chr2:62713307..62714054-chr2:62723005..62723908,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233702	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11678340	0.88[AMR][1000 genomes]
rs11686597	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11690138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11692210	0.81[AMR][1000 genomes]
rs12988497	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12989129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12998202	0.81[AMR][1000 genomes]
rs34264648	0.90[AMR][1000 genomes]
rs34282247	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36006708	0.88[AMR][1000 genomes]
rs4608498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545946	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs66636810	0.81[AMR][1000 genomes]
rs72805579	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72805589	0.88[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	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv2751	chr2:62691264-62737131	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62703600-62724800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:62705800-62732200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:62706600-62726600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:62713400-62732400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:62714000-62728000	Weak transcription	Brain Anterior Caudate	brain
6	chr2:62714200-62732400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:62714400-62728400	Weak transcription	HMEC	breast
8	chr2:62716600-62728200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:62716600-62732200	Weak transcription	Brain Angular Gyrus	brain
10	chr2:62716600-62732400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr2:62716800-62732000	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:62717200-62728800	Weak transcription	NHDF-Ad	bronchial
13	chr2:62717600-62732400	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:62717600-62732600	Weak transcription	Ovary	ovary
15	chr2:62719600-62732800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:62722000-62723600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:62722000-62724400	Enhancers	Liver	Liver
18	chr2:62722200-62723600	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr2:62722200-62725000	Enhancers	Fetal Lung	lung
20	chr2:62722400-62723600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:62722400-62724200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:62722600-62724000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:62722600-62728800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:62722800-62723600	Enhancers	Adipose Nuclei	Adipose
25	chr2:62723000-62724400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:62723000-62732200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:62723200-62723600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr2:62723200-62723600	Enhancers	A549	lung
29	chr2:62723200-62724600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:62723200-62728400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:62723400-62724600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:62723400-62724600	Weak transcription	HepG2	liver
33	chr2:62723400-62726200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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