Variant report

Variant	rs16840309
Chromosome Location	chr3:133109606-133109607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133103166..133105237-chr3:133107966..133110867,2	MCF-7	breast:

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1708373	0.82[CHD][hapmap]
rs1842156	0.86[GIH][hapmap]
rs7650741	0.82[CHD][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	nsv460857	chr3:133101390-133122216	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv591801	chr3:133101390-133122216	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16840309	TOPBP1	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133094800-133110400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:133099000-133117000	Weak transcription	Placenta	Placenta
3	chr3:133099600-133122600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:133100800-133111600	Weak transcription	HSMMtube	muscle
5	chr3:133102400-133112400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:133103400-133111600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:133103400-133112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:133103400-133115200	Weak transcription	Lung	lung
9	chr3:133103400-133123200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:133103400-133123600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:133103800-133109800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:133103800-133112000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:133103800-133115800	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:133103800-133118600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:133103800-133123800	Weak transcription	Brain Anterior Caudate	brain
16	chr3:133104000-133112000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:133104000-133122200	Weak transcription	Brain Substantia Nigra	brain
18	chr3:133104400-133112000	Strong transcription	Fetal Brain Female	brain
19	chr3:133104400-133131400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:133107200-133123800	Weak transcription	Fetal Thymus	thymus
21	chr3:133108000-133115200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:133108200-133110200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:133108200-133112800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:133108800-133112800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:133109000-133110400	Strong transcription	Fetal Lung	lung
26	chr3:133109000-133110800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:133109000-133110800	Strong transcription	HSMM	muscle
28	chr3:133109000-133111000	Strong transcription	Fetal Stomach	stomach
29	chr3:133109000-133112800	Strong transcription	Brain Germinal Matrix	brain
30	chr3:133109200-133110000	Strong transcription	Brain Angular Gyrus	brain
31	chr3:133109200-133111800	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:133109400-133110200	Strong transcription	Fetal Brain Male	brain
33	chr3:133109400-133111800	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:133109600-133110200	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:133109600-133110800	Enhancers	HepG2	liver

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