Variant report

Variant	rs7373253
Chromosome Location	chr3:53789594-53789595
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1020820	0.92[CEU][hapmap]
rs1020821	0.92[CEU][hapmap]
rs1809282	0.93[CEU][hapmap];0.88[GIH][hapmap];0.85[EUR][1000 genomes]
rs2015263	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2016271	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs2169143	0.92[CEU][hapmap]
rs2169144	0.92[CEU][hapmap]
rs2577325	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs2577327	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2577328	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2577329	0.95[EUR][1000 genomes]
rs2577331	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2612023	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2612024	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2612025	0.93[CEU][hapmap];0.88[GIH][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs2612026	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs2612029	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2612030	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2612033	0.92[CEU][hapmap];0.94[GIH][hapmap]
rs2612034	0.92[CEU][hapmap]
rs2633725	0.92[CEU][hapmap];0.94[GIH][hapmap]
rs2633727	0.92[CEU][hapmap];0.94[GIH][hapmap]
rs2680649	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs2680651	0.88[EUR][1000 genomes]
rs2680652	0.91[CEU][hapmap]
rs2680664	0.92[CEU][hapmap]
rs2680669	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs2680670	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs3774554	0.91[CEU][hapmap]
rs71616808	0.81[EUR][1000 genomes]
rs7373113	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs755886	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs7649275	0.92[CEU][hapmap];0.94[GIH][hapmap]
rs877257	0.92[CEU][hapmap];0.98[EUR][1000 genomes]
rs898419	1.00[CEU][hapmap];0.87[EUR][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	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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53768600-53801000	Strong transcription	Fetal Lung	lung
2	chr3:53773000-53807600	Strong transcription	Fetal Intestine Large	intestine
3	chr3:53774800-53807200	Strong transcription	Fetal Intestine Small	intestine
4	chr3:53778600-53806400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:53778800-53797000	Weak transcription	Pancreas	Pancrea
6	chr3:53779000-53806400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:53780400-53807000	Weak transcription	Fetal Brain Female	brain
8	chr3:53781800-53807400	Weak transcription	Brain Anterior Caudate	brain
9	chr3:53783800-53790000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:53785000-53811200	Weak transcription	Spleen	Spleen
11	chr3:53785400-53795400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:53785800-53806600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:53786000-53795600	Weak transcription	Brain Angular Gyrus	brain
14	chr3:53786000-53808200	Weak transcription	Liver	Liver
15	chr3:53787000-53790000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:53787200-53789600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:53787800-53792800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:53788200-53797400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:53788600-53795600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:53788800-53795200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:53788800-53798400	Weak transcription	Lung	lung
22	chr3:53788800-53807000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:53789200-53789800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:53789400-53789600	Enhancers	Primary T cells fromperipheralblood	blood
25	chr3:53789400-53791000	Weak transcription	Fetal Kidney	kidney
26	chr3:53789400-53797600	Weak transcription	Fetal Brain Male	brain

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