Variant report

Variant	rs66495987
Chromosome Location	chr2:64540113-64540114
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:64369964..64372694-chr2:64539391..64541388,2	MCF-7	breast:
2	chr2:64276612..64277598-chr2:64539193..64540210,6	MCF-7	breast:
3	chr2:64277766..64278422-chr2:64539629..64540166,2	MCF-7	breast:
4	chr2:64277797..64280331-chr2:64538007..64540114,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197329	Chromatin interaction
ENSG00000225889	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12463946	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12464043	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12469413	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12475531	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12990348	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13013389	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13015766	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13025947	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13029773	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17740892	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1863603	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34631419	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35503140	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36121288	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67166439	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67932764	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs737470	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7568533	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005492	chr2:64452441-64588323	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
4	nsv834244	chr2:64480943-64646259	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64537600-64540200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:64537600-64540200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:64537600-64540200	Enhancers	Fetal Thymus	thymus
4	chr2:64537600-64540200	Enhancers	HMEC	breast
5	chr2:64537600-64540800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:64537800-64540200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:64537800-64540800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:64537800-64540800	Enhancers	Fetal Muscle Leg	muscle
9	chr2:64537800-64540800	Enhancers	Fetal Stomach	stomach
10	chr2:64538000-64540200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:64538000-64540200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:64538000-64540600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:64538000-64540600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr2:64538200-64540200	Enhancers	Fetal Intestine Large	intestine
15	chr2:64538200-64540600	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr2:64538200-64540800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr2:64538200-64543800	Enhancers	Fetal Brain Male	brain
18	chr2:64538400-64540800	Enhancers	H1 Cell Line	embryonic stem cell
19	chr2:64538400-64540800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:64538600-64540200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:64538600-64540600	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr2:64538600-64540800	Enhancers	Fetal Lung	lung
23	chr2:64538600-64540800	Enhancers	Left Ventricle	heart
24	chr2:64538800-64540200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:64538800-64540800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr2:64538800-64540800	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr2:64538800-64540800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr2:64538800-64540800	Enhancers	Colon Smooth Muscle	Colon
29	chr2:64538800-64540800	Enhancers	Fetal Muscle Trunk	muscle
30	chr2:64539000-64540200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:64539000-64540200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:64539000-64540200	Flanking Active TSS	Osteobl	bone
33	chr2:64539200-64540200	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr2:64539200-64540200	Enhancers	Fetal Kidney	kidney
35	chr2:64539200-64540200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr2:64539200-64540800	Enhancers	Psoas Muscle	Psoas
37	chr2:64539200-64540800	Enhancers	Right Ventricle	heart
38	chr2:64539400-64540200	Enhancers	Esophagus	oesophagus
39	chr2:64539400-64540200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr2:64539400-64540600	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr2:64539600-64540200	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr2:64539600-64540200	Enhancers	Brain Hippocampus Middle	brain
43	chr2:64539600-64540200	Bivalent Enhancer	HepG2	liver
44	chr2:64539600-64540200	Enhancers	HSMM	muscle
45	chr2:64539600-64540200	Bivalent Enhancer	NHDF-Ad	bronchial
46	chr2:64539600-64540800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:64539600-64540800	Enhancers	Liver	Liver
48	chr2:64539600-64540800	Enhancers	HSMMtube	muscle
49	chr2:64539800-64540200	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr2:64539800-64540200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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