Variant report

Variant	rs16889479
Chromosome Location	chr5:58552908-58552909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1031197	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10491352	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10940644	0.80[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11954668	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11959132	0.80[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11959567	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12189022	0.91[EUR][1000 genomes]
rs12518773	0.92[ASN][1000 genomes]
rs12519611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12521263	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12522944	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1445948	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1445952	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1445953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1445954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1579848	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1579849	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16889499	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889518	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17444185	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17528522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17528578	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17628114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17780175	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1823070	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1838733	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1840846	0.90[EUR][1000 genomes]
rs1867711	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867712	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1947095	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2021775	1.00[JPT][hapmap]
rs2028836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2081106	1.00[JPT][hapmap]
rs2409631	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4699939	0.90[YRI][hapmap];0.94[AFR][1000 genomes]
rs4700325	1.00[JPT][hapmap]
rs4700328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6858946	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6877508	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6888028	0.86[ASN][1000 genomes]
rs6891161	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs765182	0.84[ASN][1000 genomes]
rs7703022	1.00[CHB][hapmap]
rs7717303	0.86[ASN][1000 genomes]
rs7719441	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	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
3	nsv520721	chr5:58520735-58558388	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58537600-58553000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr5:58541200-58558400	Weak transcription	Pancreas	Pancrea
3	chr5:58541600-58560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:58541600-58562400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr5:58541800-58562800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:58544400-58553000	Weak transcription	Left Ventricle	heart
7	chr5:58549000-58553800	Weak transcription	Stomach Mucosa	stomach
8	chr5:58549000-58555200	Weak transcription	Hela-S3	cervix
9	chr5:58549800-58553200	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr5:58550400-58553200	Weak transcription	HepG2	liver
11	chr5:58551400-58554200	Enhancers	Fetal Kidney	kidney
12	chr5:58551400-58557600	Enhancers	Rectal Smooth Muscle	rectum
13	chr5:58551600-58553200	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr5:58551600-58553600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:58551600-58553600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:58551800-58554200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr5:58551800-58554200	Flanking Active TSS	A549	lung
18	chr5:58552000-58553000	Enhancers	Brain Cingulate Gyrus	brain
19	chr5:58552200-58556800	Weak transcription	Brain Substantia Nigra	brain
20	chr5:58552400-58553000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr5:58552400-58553200	Weak transcription	Fetal Heart	heart
22	chr5:58552400-58553600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr5:58552400-58553800	Enhancers	Right Atrium	heart
24	chr5:58552400-58554200	Enhancers	Psoas Muscle	Psoas
25	chr5:58552400-58555200	Enhancers	Colon Smooth Muscle	Colon
26	chr5:58552400-58555200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr5:58552400-58558400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:58552600-58556600	Weak transcription	Brain Angular Gyrus	brain
29	chr5:58552600-58560400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:58552800-58553200	Weak transcription	Fetal Lung	lung
31	chr5:58552800-58554200	Enhancers	Fetal Intestine Large	intestine

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