Variant report

Variant	rs16889499
Chromosome Location	chr5:58560338-58560339
allele	C/T
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:34)

rs_ID	r²[population]
rs10491352	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10940644	0.82[EUR][1000 genomes]
rs11959132	0.82[EUR][1000 genomes]
rs12189022	0.92[EUR][1000 genomes]
rs12518773	0.92[ASN][1000 genomes]
rs12519611	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12521263	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12522944	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1445948	0.86[ASN][1000 genomes]
rs1445952	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1445953	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1445954	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1579848	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1579849	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16889479	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889518	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17444185	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17528522	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17528578	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17628114	0.83[ASN][1000 genomes]
rs1823070	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1840846	0.91[EUR][1000 genomes]
rs1867711	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867712	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947090	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1947095	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2028836	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4699939	0.93[AFR][1000 genomes]
rs4700328	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6858946	0.86[ASN][1000 genomes]
rs6877508	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6888028	0.86[ASN][1000 genomes]
rs765182	0.84[ASN][1000 genomes]
rs7717303	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58541600-58562400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:58541800-58562800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58552600-58560400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:58553800-58568600	Weak transcription	Fetal Muscle Leg	muscle
5	chr5:58554200-58561000	Weak transcription	Stomach Mucosa	stomach
6	chr5:58554200-58562600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr5:58557200-58560600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:58557200-58562400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:58557400-58560600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:58558000-58560600	Weak transcription	Fetal Intestine Large	intestine
11	chr5:58558000-58561000	Weak transcription	Fetal Intestine Small	intestine
12	chr5:58558400-58564400	Enhancers	Fetal Heart	heart
13	chr5:58558600-58560600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:58558600-58561000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:58559200-58560600	Weak transcription	Left Ventricle	heart
16	chr5:58559200-58560600	Weak transcription	Right Atrium	heart
17	chr5:58559200-58561000	Enhancers	Hela-S3	cervix
18	chr5:58559200-58562200	Weak transcription	Psoas Muscle	Psoas
19	chr5:58559200-58564200	Weak transcription	Pancreas	Pancrea
20	chr5:58559400-58561400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:58559600-58560800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr5:58559800-58560600	Enhancers	Colon Smooth Muscle	Colon
23	chr5:58559800-58561800	Flanking Active TSS	A549	lung
24	chr5:58559800-58562400	Weak transcription	Colonic Mucosa	Colon
25	chr5:58560000-58560400	Enhancers	Fetal Lung	lung
26	chr5:58560000-58560400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr5:58560000-58560600	Enhancers	Fetal Brain Female	brain
28	chr5:58560000-58561000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:58560000-58561200	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr5:58560000-58561200	Enhancers	HSMMtube	muscle
31	chr5:58560200-58561000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:58560200-58561800	Enhancers	Placenta Amnion	Placenta Amnion
33	chr5:58560200-58566600	Enhancers	Rectal Smooth Muscle	rectum

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