Variant report

Variant	rs1449088
Chromosome Location	chr2:187582569-187582570
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:187558747..187561002-chr2:187582071..187584698,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227227	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1349170	1.00[EUR][1000 genomes]
rs1375447	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1449090	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1449091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1470602	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16828026	1.00[CHB][hapmap]
rs16828108	1.00[CHB][hapmap]
rs16828136	0.85[ASN][1000 genomes]
rs1839122	1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2122177	1.00[EUR][1000 genomes]
rs2167013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2247924	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2442316	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2442318	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2594702	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2594703	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2594704	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2595377	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2595379	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2595388	1.00[EUR][1000 genomes]
rs2682852	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2682853	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2682854	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682858	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2682859	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2682860	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2682861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2682866	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682869	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2682870	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2682872	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682874	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738918	1.00[CHB][hapmap]
rs3754584	1.00[CHB][hapmap]
rs4309547	1.00[EUR][1000 genomes]
rs57306419	1.00[EUR][1000 genomes]
rs59855103	1.00[EUR][1000 genomes]
rs6761687	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73035695	1.00[EUR][1000 genomes]
rs7556971	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs976693	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428069	chr2:187575692-187766209	ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187560600-187584200	Weak transcription	Fetal Lung	lung
2	chr2:187576200-187582600	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr2:187578000-187583600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:187578800-187583800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:187579200-187583800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:187581200-187583600	Enhancers	Brain Angular Gyrus	brain
7	chr2:187581200-187584400	Enhancers	Brain Hippocampus Middle	brain
8	chr2:187581600-187582600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:187581600-187583800	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr2:187581600-187584400	Enhancers	Brain Cingulate Gyrus	brain
11	chr2:187581600-187584600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:187581600-187584600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr2:187581800-187584600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:187582000-187582600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:187582000-187583600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr2:187582000-187583800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr2:187582000-187583800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr2:187582000-187584200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:187582000-187584600	Enhancers	Brain Anterior Caudate	brain
20	chr2:187582200-187582600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr2:187582200-187582600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:187582200-187582600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:187582200-187582600	Flanking Active TSS	Fetal Brain Female	brain
24	chr2:187582200-187584000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr2:187582200-187584200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr2:187582200-187584400	Enhancers	Brain Germinal Matrix	brain
27	chr2:187582200-187584600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr2:187582200-187584600	Enhancers	Fetal Brain Male	brain
29	chr2:187582400-187582600	Flanking Active TSS	Brain Substantia Nigra	brain
30	chr2:187582400-187583000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr2:187582400-187583800	Enhancers	H9 Cell Line	embryonic stem cell
32	chr2:187582400-187584400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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