Variant report

Variant	rs62283348
Chromosome Location	chr3:177406153-177406154
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	chr3:177398506..177400476-chr3:177405856..177408346,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10513751	0.91[EUR][1000 genomes]
rs11707843	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12486651	0.93[EUR][1000 genomes]
rs12487647	0.93[EUR][1000 genomes]
rs12493064	0.92[EUR][1000 genomes]
rs12631987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12633573	0.93[EUR][1000 genomes]
rs12638525	1.00[ASN][1000 genomes]
rs1392197	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1392198	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16828483	0.93[EUR][1000 genomes]
rs16828521	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848236	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1846585	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1846586	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34585605	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56673356	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57793263	0.93[EUR][1000 genomes]
rs62283317	0.93[EUR][1000 genomes]
rs62283321	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62283322	0.93[EUR][1000 genomes]
rs62283323	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62283343	0.93[EUR][1000 genomes]
rs62283344	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62283346	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62283349	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283351	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283352	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283356	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6766877	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768558	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6782388	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6783540	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67889675	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6798789	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800850	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802610	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73174869	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73174897	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7634114	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7646007	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648462	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648551	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651286	0.93[EUR][1000 genomes]
rs9681874	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	esv2752972	chr3:176924298-177425298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv931055	chr3:177229521-177889872	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv998537	chr3:177403421-177425648	Flanking Active TSS Weak transcription Enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1009087	chr3:177405231-177422275	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:177392400-177418800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:177395000-177411600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:177398800-177421600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:177400400-177406200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:177405200-177407000	Enhancers	Brain Hippocampus Middle	brain
6	chr3:177405400-177406800	Enhancers	Brain Anterior Caudate	brain
7	chr3:177405400-177406800	Enhancers	Brain Cingulate Gyrus	brain
8	chr3:177405400-177406800	Enhancers	Brain Substantia Nigra	brain
9	chr3:177405600-177406200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:177405600-177411400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:177405800-177406400	Enhancers	Brain Germinal Matrix	brain
12	chr3:177405800-177406600	Enhancers	Colon Smooth Muscle	Colon
13	chr3:177405800-177411600	Weak transcription	Fetal Brain Male	brain
14	chr3:177406000-177406200	Enhancers	Brain Angular Gyrus	brain
15	chr3:177406000-177406400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
16	chr3:177406000-177406600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:177406000-177406600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:177406000-177407000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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