Variant report

Variant	rs28540859
Chromosome Location	chr5:58483294-58483295
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10036938	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10042606	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10077198	0.86[ASN][1000 genomes]
rs10472094	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10472095	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948460	0.86[ASN][1000 genomes]
rs12108992	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12516263	0.93[ASN][1000 genomes]
rs13357070	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889248	0.80[ASN][1000 genomes]
rs16889254	0.89[ASN][1000 genomes]
rs16889258	0.93[ASN][1000 genomes]
rs28705844	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62357974	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450504	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450505	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450508	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450509	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6868963	0.86[ASN][1000 genomes]
rs6869149	0.93[ASN][1000 genomes]
rs6874089	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6883912	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6892369	0.93[ASN][1000 genomes]
rs6896497	1.00[ASN][1000 genomes]
rs7700594	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714707	0.93[ASN][1000 genomes]
rs7728221	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7735375	0.93[ASN][1000 genomes]
rs922436	0.96[ASN][1000 genomes]
rs9292191	0.93[ASN][1000 genomes]
rs9918111	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58439000-58484000	Weak transcription	Fetal Kidney	kidney
2	chr5:58449800-58489400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:58461000-58484200	Weak transcription	HUVEC	blood vessel
4	chr5:58464200-58484000	Weak transcription	Brain Anterior Caudate	brain
5	chr5:58464200-58485400	Weak transcription	Aorta	Aorta
6	chr5:58469000-58483800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr5:58469200-58484400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr5:58470000-58483400	Weak transcription	Fetal Lung	lung
9	chr5:58470600-58483800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:58471000-58483600	Weak transcription	Brain Angular Gyrus	brain
11	chr5:58471000-58483800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr5:58471000-58484800	Weak transcription	Pancreas	Pancrea
13	chr5:58471600-58484200	Weak transcription	Brain Germinal Matrix	brain
14	chr5:58472000-58484400	Weak transcription	Primary B cells from cord blood	blood
15	chr5:58472200-58485800	Weak transcription	Stomach Mucosa	stomach
16	chr5:58472800-58484200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr5:58474400-58520000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:58474600-58483600	Weak transcription	Fetal Brain Female	brain
19	chr5:58474600-58484400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr5:58474800-58484400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr5:58474800-58484800	Weak transcription	Fetal Intestine Small	intestine
22	chr5:58474800-58491000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:58475000-58484400	Weak transcription	Right Ventricle	heart
24	chr5:58475200-58484200	Weak transcription	Fetal Stomach	stomach
25	chr5:58475800-58484800	Weak transcription	Fetal Intestine Large	intestine
26	chr5:58476800-58484200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr5:58478400-58483600	Weak transcription	Fetal Brain Male	brain
28	chr5:58478800-58483400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:58478800-58484400	Strong transcription	Hela-S3	cervix
30	chr5:58479400-58483600	Weak transcription	HSMMtube	muscle
31	chr5:58479400-58483800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr5:58479600-58483600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr5:58479600-58483600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:58479800-58483600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:58479800-58483600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr5:58479800-58484000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr5:58479800-58484400	Weak transcription	Fetal Muscle Leg	muscle
38	chr5:58479800-58487200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr5:58479800-58489800	Weak transcription	Gastric	stomach
40	chr5:58480000-58483800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr5:58480000-58483800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr5:58480000-58484000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr5:58480000-58485400	Weak transcription	Left Ventricle	heart
44	chr5:58480200-58488800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr5:58481000-58483800	Weak transcription	Fetal Heart	heart
46	chr5:58481000-58486600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr5:58481800-58483800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr5:58482000-58484000	Enhancers	Rectal Smooth Muscle	rectum
49	chr5:58482200-58484600	Weak transcription	Psoas Muscle	Psoas
50	chr5:58482400-58483800	Weak transcription	Placenta Amnion	Placenta Amnion

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