Variant report

Variant	rs3733073
Chromosome Location	chr3:53886633-53886634
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10440151	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1046677	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1134092	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1157175	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13072145	0.83[ASN][1000 genomes]
rs13315972	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1982172	0.81[EUR][1000 genomes]
rs1992155	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2083127	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2276846	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3733081	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3816144	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3821867	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4569647	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687757	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687763	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7624599	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7636856	0.83[ASN][1000 genomes]
rs893367	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9311516	0.83[ASN][1000 genomes]
rs9311518	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9822471	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9840079	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9840362	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9869505	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9878207	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9878562	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs999514	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv876803	chr3:53822893-53889849	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3733073	SELK	Cis_1M	lymphoblastoid	RTeQTL
rs3733073	IL17RB	cis	Whole Blood	GTEx
rs3733073	IL17RB	cis	Artery Tibial	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53881000-53892600	Weak transcription	Psoas Muscle	Psoas
2	chr3:53881000-53893200	Weak transcription	Ovary	ovary
3	chr3:53881200-53892400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:53881200-53895000	Weak transcription	A549	lung
5	chr3:53881200-53895800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:53881400-53887000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:53881400-53887200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:53881400-53887400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:53881400-53889200	Weak transcription	Fetal Intestine Small	intestine
10	chr3:53881400-53891400	Weak transcription	Brain Anterior Caudate	brain
11	chr3:53881400-53892000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:53881400-53892000	Weak transcription	Gastric	stomach
13	chr3:53881400-53892200	Weak transcription	Fetal Intestine Large	intestine
14	chr3:53881400-53892200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:53881400-53892600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:53881400-53892600	Weak transcription	Hela-S3	cervix
17	chr3:53881400-53892800	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:53881400-53893000	Weak transcription	Brain Angular Gyrus	brain
19	chr3:53881400-53893000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:53881600-53887000	Weak transcription	Liver	Liver
21	chr3:53882400-53886800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:53882400-53891400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:53882600-53892200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:53882800-53892200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:53883000-53891000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr3:53883200-53887600	Weak transcription	Pancreas	Pancrea
27	chr3:53883200-53889400	Weak transcription	GM12878-XiMat	blood
28	chr3:53884000-53887600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:53884000-53895800	Strong transcription	HepG2	liver
30	chr3:53884400-53892200	Weak transcription	Fetal Brain Female	brain
31	chr3:53884400-53892800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:53885000-53901000	Weak transcription	Fetal Heart	heart
33	chr3:53885200-53887800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:53885200-53892200	Weak transcription	Fetal Lung	lung
35	chr3:53885400-53891200	Weak transcription	Fetal Stomach	stomach
36	chr3:53885400-53892400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:53885400-53892800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:53885400-53895200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:53885600-53892200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:53885600-53892600	Weak transcription	Left Ventricle	heart
41	chr3:53885600-53896600	Weak transcription	Right Ventricle	heart
42	chr3:53886000-53887800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:53886200-53888000	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr3:53886200-53897200	Weak transcription	Colonic Mucosa	Colon
45	chr3:53886600-53887800	Strong transcription	Brain Substantia Nigra	brain

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