Variant report

Variant	rs12488406
Chromosome Location	chr3:116111151-116111152
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1073924	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10804523	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12492517	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1367772	0.85[EUR][1000 genomes]
rs1920184	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1920186	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1920190	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2033406	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4831131	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6786250	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9823782	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9870357	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[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	nsv877361	chr3:116017931-116138039	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv2757005	chr3:116085678-116121948	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	esv2759170	chr3:116085678-116121948	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1003543	chr3:116096198-116111430	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:116103000-116142000	Weak transcription	Fetal Lung	lung
2	chr3:116108000-116113400	Weak transcription	Brain Angular Gyrus	brain
3	chr3:116108200-116115200	Weak transcription	Brain Anterior Caudate	brain
4	chr3:116108400-116112800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:116108400-116113400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:116108400-116113600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:116108600-116113200	Weak transcription	Brain Substantia Nigra	brain
8	chr3:116108600-116113800	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:116108600-116114200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:116109200-116118600	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:116109600-116118400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:116110600-116111800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:116110600-116112200	ZNF genes & repeats	Brain Germinal Matrix	brain
14	chr3:116110600-116112200	ZNF genes & repeats	Fetal Stomach	stomach
15	chr3:116110600-116112400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:116110600-116112600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
17	chr3:116110800-116112000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:116111000-116111200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr3:116111000-116111400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:116111000-116112600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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