Variant report

Variant	rs13078406
Chromosome Location	chr3:43024005-43024006
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	chr3:43017736..43019452-chr3:43022263..43024227,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12494055	0.83[JPT][hapmap]
rs13081156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13081266	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17388512	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2288370	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36132109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3732860	0.83[JPT][hapmap]
rs55946409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6788947	0.83[JPT][hapmap]
rs9812262	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43021400-43030200	Weak transcription	Aorta	Aorta
2	chr3:43021600-43024600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:43022000-43033000	Weak transcription	Pancreas	Pancrea
4	chr3:43022000-43037000	Weak transcription	Right Atrium	heart
5	chr3:43022200-43027600	Weak transcription	Placenta	Placenta
6	chr3:43022200-43032800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:43022400-43026800	Weak transcription	Brain Substantia Nigra	brain
8	chr3:43022800-43025000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:43022800-43025200	Weak transcription	Brain Anterior Caudate	brain
10	chr3:43022800-43027600	Weak transcription	Fetal Intestine Small	intestine
11	chr3:43022800-43030000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:43023000-43037800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:43023200-43024200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:43023200-43024200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:43023200-43024200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:43023200-43029600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:43023400-43026400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:43023400-43029600	Weak transcription	Liver	Liver
19	chr3:43023800-43025400	Enhancers	Ovary	ovary
20	chr3:43024000-43024400	Enhancers	Fetal Lung	lung
21	chr3:43024000-43026600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr3:43024000-43027400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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