Variant report

Variant	rs12497288
Chromosome Location	chr3:49670650-49670651
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1060962	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11130212	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11919311	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12490267	0.93[EUR][1000 genomes]
rs1352890	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1873626	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2005557	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2131104	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2131109	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2329020	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2960548	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35007338	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35404120	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4855835	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4855847	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4855852	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4855881	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4855883	0.85[EUR][1000 genomes]
rs4855884	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6765869	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6767878	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv3812	chr3:49669773-49680587	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49655600-49676200	Weak transcription	HepG2	liver
2	chr3:49657600-49685400	Weak transcription	Brain Substantia Nigra	brain
3	chr3:49660800-49682600	Weak transcription	Liver	Liver
4	chr3:49661600-49692400	Weak transcription	Ovary	ovary
5	chr3:49661800-49682200	Weak transcription	Fetal Brain Male	brain
6	chr3:49662800-49685000	Weak transcription	Right Ventricle	heart
7	chr3:49663800-49679600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:49664200-49683200	Weak transcription	Pancreas	Pancrea
9	chr3:49664600-49674000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:49664600-49680000	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:49665000-49672400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:49665600-49673800	Weak transcription	Brain Angular Gyrus	brain
13	chr3:49667200-49674000	Weak transcription	Brain Anterior Caudate	brain
14	chr3:49667600-49679800	Weak transcription	Brain Germinal Matrix	brain
15	chr3:49668000-49673800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:49669400-49674200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:49669400-49692000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:49669600-49679400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:49669600-49679800	Weak transcription	Fetal Brain Female	brain
20	chr3:49669600-49680000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:49670000-49680000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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