Variant report

Variant	rs58509921
Chromosome Location	chr13:96559389-96559390
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13378684	0.86[AFR][1000 genomes]
rs28503176	0.85[ASN][1000 genomes]
rs28625167	0.82[ASN][1000 genomes]
rs28631067	0.91[ASN][1000 genomes]
rs28895285	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35405829	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3782991	0.83[AFR][1000 genomes]
rs3825423	0.86[AFR][1000 genomes]
rs4406928	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4550324	0.85[ASN][1000 genomes]
rs61152555	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61422359	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7327257	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7330135	0.87[ASN][1000 genomes]
rs7988464	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7990333	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7990743	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9584330	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9584331	0.84[AFR][1000 genomes]
rs9584332	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9584335	0.86[AFR][1000 genomes]
rs9590329	0.85[ASN][1000 genomes]
rs9590335	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9590338	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9590340	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9590341	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9590351	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9590352	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9590353	0.81[ASN][1000 genomes]
rs9590354	0.83[AFR][1000 genomes]

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	nsv832691	chr13:96478098-96659823	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv900935	chr13:96497070-96631221	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1051574	chr13:96550653-96779248	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96478000-96568400	Weak transcription	Placenta	Placenta
2	chr13:96495000-96590800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:96502800-96562600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr13:96503000-96567400	Weak transcription	NHEK	skin
5	chr13:96503400-96580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr13:96503600-96562800	Weak transcription	Fetal Brain Female	brain
7	chr13:96523200-96581800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr13:96524000-96561200	Weak transcription	HMEC	breast
9	chr13:96524200-96560400	Weak transcription	Brain Angular Gyrus	brain
10	chr13:96536200-96587200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr13:96539400-96561200	Weak transcription	NH-A	brain
12	chr13:96542400-96576800	Weak transcription	HSMMtube	muscle
13	chr13:96542400-96581600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr13:96543000-96581600	Weak transcription	Fetal Lung	lung
15	chr13:96543000-96581800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr13:96543000-96586800	Weak transcription	Brain Hippocampus Middle	brain
17	chr13:96543400-96576600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr13:96544600-96576800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr13:96549000-96563200	Weak transcription	Stomach Mucosa	stomach
20	chr13:96549400-96586400	Weak transcription	Hela-S3	cervix
21	chr13:96553200-96573600	Weak transcription	Osteobl	bone
22	chr13:96555800-96561000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr13:96556400-96563000	Weak transcription	Fetal Heart	heart
24	chr13:96558000-96559400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr13:96558000-96559400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr13:96558000-96559400	Strong transcription	HSMM	muscle
27	chr13:96558000-96559600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
28	chr13:96558000-96560200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
29	chr13:96558200-96559400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
30	chr13:96558200-96559400	ZNF genes & repeats	Liver	Liver
31	chr13:96558200-96559800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr13:96558200-96560000	ZNF genes & repeats	Fetal Muscle Leg	muscle
33	chr13:96558400-96559600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr13:96558400-96560000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr13:96558400-96567200	Weak transcription	Fetal Kidney	kidney
36	chr13:96558400-96586600	Weak transcription	Right Ventricle	heart
37	chr13:96558600-96559400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
38	chr13:96558600-96579000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr13:96558800-96559600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr13:96558800-96559600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr13:96558800-96560000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
42	chr13:96558800-96560400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr13:96559000-96559400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
44	chr13:96559000-96559400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
45	chr13:96559000-96559600	ZNF genes & repeats	Fetal Intestine Small	intestine
46	chr13:96559000-96559600	Strong transcription	Pancreas	Pancrea
47	chr13:96559000-96559600	Strong transcription	A549	lung
48	chr13:96559000-96559800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
49	chr13:96559000-96559800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr13:96559000-96559800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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