Variant report

Variant	rs9835258
Chromosome Location	chr3:53887931-53887932
allele	A/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:30)

rs_ID	r²[population]
rs11130383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11130384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11562	0.83[AFR][1000 genomes]
rs12715465	1.00[AMR][1000 genomes]
rs13321898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13322337	1.00[AMR][1000 genomes]
rs13434145	1.00[AMR][1000 genomes]
rs28409957	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6782007	1.00[AMR][1000 genomes]
rs6785238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6802878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72556356	1.00[AMR][1000 genomes]
rs7614233	1.00[AMR][1000 genomes]
rs7636496	1.00[AMR][1000 genomes]
rs7637908	1.00[AMR][1000 genomes]
rs7640840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9814675	1.00[AMR][1000 genomes]
rs9816010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9818571	1.00[AMR][1000 genomes]
rs9823141	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9830672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9833359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9834168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9849610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9852243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9859937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9860224	1.00[AMR][1000 genomes]
rs9872403	1.00[AMR][1000 genomes]
rs9878250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9882134	0.91[AFR][1000 genomes];1.00[AMR][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

No data

Chromatin state (count:47 , 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	chr3:53881400-53889200	Weak transcription	Fetal Intestine Small	intestine
7	chr3:53881400-53891400	Weak transcription	Brain Anterior Caudate	brain
8	chr3:53881400-53892000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:53881400-53892000	Weak transcription	Gastric	stomach
10	chr3:53881400-53892200	Weak transcription	Fetal Intestine Large	intestine
11	chr3:53881400-53892200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:53881400-53892600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:53881400-53892600	Weak transcription	Hela-S3	cervix
14	chr3:53881400-53892800	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:53881400-53893000	Weak transcription	Brain Angular Gyrus	brain
16	chr3:53881400-53893000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:53882400-53891400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:53882600-53892200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:53882800-53892200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:53883000-53891000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:53883200-53889400	Weak transcription	GM12878-XiMat	blood
22	chr3:53884000-53895800	Strong transcription	HepG2	liver
23	chr3:53884400-53892200	Weak transcription	Fetal Brain Female	brain
24	chr3:53884400-53892800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:53885000-53901000	Weak transcription	Fetal Heart	heart
26	chr3:53885200-53892200	Weak transcription	Fetal Lung	lung
27	chr3:53885400-53891200	Weak transcription	Fetal Stomach	stomach
28	chr3:53885400-53892400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:53885400-53892800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:53885400-53895200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:53885600-53892200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:53885600-53892600	Weak transcription	Left Ventricle	heart
33	chr3:53885600-53896600	Weak transcription	Right Ventricle	heart
34	chr3:53886200-53888000	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr3:53886200-53897200	Weak transcription	Colonic Mucosa	Colon
36	chr3:53887200-53888800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:53887400-53888800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:53887600-53891200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:53887600-53892400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:53887800-53889600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:53887800-53889600	Weak transcription	Liver	Liver
42	chr3:53887800-53889600	Weak transcription	Pancreas	Pancrea
43	chr3:53887800-53890600	Weak transcription	Brain Substantia Nigra	brain
44	chr3:53887800-53891000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:53887800-53891200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:53887800-53892800	Weak transcription	Lung	lung
47	chr3:53887800-53898400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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