Variant report

Variant	rs12490267
Chromosome Location	chr3:49657852-49657853
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	chr3:49656466..49658161-chr3:49661338..49664301,2	MCF-7	breast:
2	chr3:49656091..49658798-chr3:49660626..49662270,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1060962	0.87[EUR][1000 genomes]
rs11130212	0.87[EUR][1000 genomes]
rs11919311	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12497288	0.93[EUR][1000 genomes]
rs1352890	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1873626	0.92[EUR][1000 genomes]
rs2005557	0.87[EUR][1000 genomes]
rs2131104	0.87[EUR][1000 genomes]
rs2131109	0.87[EUR][1000 genomes]
rs2329020	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2960548	0.85[EUR][1000 genomes]
rs35007338	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35404120	0.87[EUR][1000 genomes]
rs4855835	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4855847	0.88[EUR][1000 genomes]
rs4855852	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4855881	0.85[EUR][1000 genomes]
rs4855883	0.83[EUR][1000 genomes]
rs4855884	0.87[EUR][1000 genomes]
rs6765869	0.86[EUR][1000 genomes]

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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49648400-49662000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:49654000-49662400	Weak transcription	Fetal Brain Female	brain
3	chr3:49654200-49662600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:49654400-49668200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:49654600-49662200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:49654600-49662400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:49654600-49662600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:49654600-49662600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:49654600-49663600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:49654600-49664200	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:49655000-49668800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:49655600-49676200	Weak transcription	HepG2	liver
13	chr3:49657200-49662400	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:49657400-49658600	Weak transcription	NH-A	brain
15	chr3:49657400-49662200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:49657400-49662400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:49657600-49662600	Weak transcription	Brain Angular Gyrus	brain
18	chr3:49657600-49662600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:49657600-49663400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:49657600-49685400	Weak transcription	Brain Substantia Nigra	brain

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