Variant report

Variant	rs2340859
Chromosome Location	chr2:151448583-151448584
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:151342117..151344556-chr2:151448432..151450582,2	MCF-7	breast:
2	chr13:26681491..26682293-chr2:151448480..151449368,2	MCF-7	breast:
3	chr2:151338773..151340469-chr2:151447242..151449602,2	MCF-7	breast:
4	chr2:151446443..151448791-chr2:151456173..151458106,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115963	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10469691	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10469692	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12615315	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2340864	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34849534	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4438475	0.80[EUR][1000 genomes]
rs4664679	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6720091	0.80[EUR][1000 genomes]
rs6757157	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7571312	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7604619	0.96[CEU][hapmap];0.94[EUR][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	nsv1001838	chr2:150819672-151745876	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv535980	chr2:150819672-151745876	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv532473	chr2:151164210-151701860	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv834415	chr2:151374254-151558649	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv275419	chr2:151447063-151452042	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151443600-151450400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:151444600-151452200	Weak transcription	NH-A	brain
3	chr2:151447200-151449400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr2:151447600-151449000	Enhancers	NHLF	lung
5	chr2:151447800-151448800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:151447800-151448800	Enhancers	Fetal Brain Male	brain
7	chr2:151447800-151449000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:151447800-151449000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:151448000-151448800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:151448000-151448800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:151448000-151449000	Enhancers	Osteobl	bone
12	chr2:151448000-151449200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr2:151448000-151449400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:151448000-151452600	Weak transcription	Fetal Brain Female	brain
15	chr2:151448200-151448800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:151448200-151448800	Enhancers	A549	lung
17	chr2:151448200-151449000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:151448200-151449000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:151448200-151449000	Flanking Active TSS	NHDF-Ad	bronchial
20	chr2:151448200-151449000	Enhancers	NHEK	skin
21	chr2:151448200-151449200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:151448200-151449200	Enhancers	HMEC	breast
23	chr2:151448400-151448800	Enhancers	HSMM	muscle
24	chr2:151448400-151452200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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