Variant report

Variant	rs2462589
Chromosome Location	chr2:47414001-47414002
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47412361..47428396-chr2:47486545..47501626,43	MCF-7	breast:
2	chr2:47413983..47416889-chr2:47539395..47542144,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs11125126	0.96[ASN][1000 genomes]
rs1404770	0.97[ASN][1000 genomes]
rs1630239	0.97[ASN][1000 genomes]
rs1693863	0.97[ASN][1000 genomes]
rs1693864	0.91[ASN][1000 genomes]
rs1693882	0.81[ASN][1000 genomes]
rs1723482	0.86[ASN][1000 genomes]
rs1995108	0.97[ASN][1000 genomes]
rs2454082	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2454083	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2462588	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713934	0.97[ASN][1000 genomes]
rs6751198	0.96[ASN][1000 genomes]
rs7606478	0.97[ASN][1000 genomes]
rs815802	0.86[ASN][1000 genomes]
rs815815	0.86[ASN][1000 genomes]
rs815817	0.96[ASN][1000 genomes]
rs878665	0.88[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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv457374	chr2:47313624-47448865	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv581754	chr2:47313624-47448865	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47404400-47418600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:47404600-47416400	Weak transcription	HSMMtube	muscle
3	chr2:47404600-47417200	Weak transcription	Placenta	Placenta
4	chr2:47404800-47416400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:47405400-47416400	Weak transcription	Fetal Intestine Large	intestine
6	chr2:47411200-47416400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:47411600-47415400	Weak transcription	NHDF-Ad	bronchial
8	chr2:47411800-47416200	Weak transcription	HSMM	muscle
9	chr2:47411800-47416400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:47412000-47415400	Weak transcription	NHLF	lung
11	chr2:47412000-47415800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:47412000-47416200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:47412000-47416200	Weak transcription	NH-A	brain
14	chr2:47412000-47416400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:47412000-47416400	Weak transcription	Osteobl	bone
16	chr2:47412400-47416400	Enhancers	A549	lung
17	chr2:47412600-47415800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:47413000-47415200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:47413200-47414800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr2:47413400-47414400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:47413600-47414400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:47413600-47415000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:47413600-47415200	Enhancers	K562	blood
24	chr2:47413800-47414600	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr2:47413800-47414800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr2:47413800-47415000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:47414000-47414400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:47414000-47417000	Weak transcription	Brain Germinal Matrix	brain
29	chr2:47414000-47417400	Weak transcription	Brain Substantia Nigra	brain

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