Variant report

Variant	rs2633725
Chromosome Location	chr3:53751742-53751743
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	chr3:53740542..53743254-chr3:53751040..53753856,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1020820	1.00[CEU][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1020821	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1809282	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs2016271	0.85[CEU][hapmap]
rs2169143	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2169144	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2577325	0.85[CEU][hapmap]
rs2577328	0.90[CEU][hapmap]
rs2577331	0.91[CEU][hapmap]
rs2612023	0.92[CEU][hapmap]
rs2612024	0.92[CEU][hapmap]
rs2612025	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs2612026	0.92[CEU][hapmap];0.94[GIH][hapmap]
rs2612029	0.91[CEU][hapmap]
rs2612030	0.92[CEU][hapmap]
rs2612032	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2612033	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2612034	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2633724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2633727	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2680649	0.92[CEU][hapmap];0.94[GIH][hapmap]
rs2680652	0.81[CEU][hapmap]
rs2680664	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2680669	0.85[CEU][hapmap]
rs2680670	0.85[CEU][hapmap]
rs3774554	0.83[CEU][hapmap]
rs7373113	0.92[CEU][hapmap]
rs7373253	0.92[CEU][hapmap];0.94[GIH][hapmap]
rs755886	0.92[CEU][hapmap];0.94[GIH][hapmap]
rs7613589	0.83[YRI][hapmap]
rs7649275	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs877257	0.85[CEU][hapmap]
rs898409	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs898419	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1007655	chr3:53742148-53767689	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1002452	chr3:53742148-53802811	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1000280	chr3:53742736-53770588	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2633725	AMIGO3	cis	parietal	SCAN
rs2633725	RAD54L2	cis	parietal	SCAN
rs2633725	RBM5	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53740200-53764400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:53742600-53778000	Weak transcription	Pancreas	Pancrea
3	chr3:53744200-53753800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:53744200-53764600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:53744400-53756600	Weak transcription	Lung	lung
6	chr3:53744400-53758600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:53744400-53763800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:53744600-53755000	Weak transcription	Brain Anterior Caudate	brain
9	chr3:53744600-53755000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:53744600-53756400	Weak transcription	Liver	Liver
11	chr3:53744600-53761200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:53745000-53753800	Strong transcription	Fetal Intestine Small	intestine
13	chr3:53745200-53762800	Strong transcription	Fetal Intestine Large	intestine
14	chr3:53748400-53752800	Weak transcription	Spleen	Spleen
15	chr3:53748600-53756200	Weak transcription	Fetal Brain Male	brain
16	chr3:53749200-53752400	Strong transcription	Fetal Lung	lung
17	chr3:53750000-53755200	Weak transcription	Left Ventricle	heart
18	chr3:53750400-53752400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:53750400-53755000	Weak transcription	NHDF-Ad	bronchial
20	chr3:53750400-53755200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:53750400-53755200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:53750600-53753400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:53750600-53755000	Weak transcription	Osteobl	bone
24	chr3:53750800-53752400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:53751000-53752000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:53751200-53755000	Weak transcription	NH-A	brain

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