Variant report

Variant	rs16889280
Chromosome Location	chr5:58446582-58446583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10038299	0.85[ASN][1000 genomes]
rs10039838	0.86[ASN][1000 genomes]
rs10085037	0.86[ASN][1000 genomes]
rs10085076	0.86[ASN][1000 genomes]
rs1105577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1551938	0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs1824788	0.86[JPT][hapmap]
rs3901540	0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs55730818	0.84[ASN][1000 genomes]
rs55998224	0.84[ASN][1000 genomes]
rs6877743	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs72764072	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7728050	0.83[CHB][hapmap]

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	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	nsv881702	chr5:58432413-58474854	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	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	chr5:58424000-58447000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:58424200-58446600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr5:58427200-58454000	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr5:58429800-58447200	Weak transcription	Left Ventricle	heart
5	chr5:58433000-58451600	Weak transcription	Fetal Muscle Leg	muscle
6	chr5:58437400-58454000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:58439000-58484000	Weak transcription	Fetal Kidney	kidney
8	chr5:58440000-58447000	Weak transcription	Stomach Mucosa	stomach
9	chr5:58440200-58448600	Weak transcription	Brain Anterior Caudate	brain
10	chr5:58440600-58447000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr5:58441200-58446600	Weak transcription	Fetal Heart	heart
12	chr5:58442400-58448600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:58443000-58447000	Weak transcription	Primary T cells from cord blood	blood
14	chr5:58443000-58447400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:58443000-58447600	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr5:58443200-58447000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr5:58443200-58447000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:58444000-58449800	Genic enhancers	A549	lung
19	chr5:58444800-58448000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr5:58444800-58448400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:58445400-58447200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:58445800-58447400	Strong transcription	Hela-S3	cervix
23	chr5:58445800-58448000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:58446000-58447200	Weak transcription	Psoas Muscle	Psoas
25	chr5:58446000-58447400	Weak transcription	Colon Smooth Muscle	Colon
26	chr5:58446000-58448000	Enhancers	Fetal Intestine Small	intestine
27	chr5:58446000-58448600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:58446200-58447400	Weak transcription	Small Intestine	intestine
29	chr5:58446200-58448400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:58446200-58449000	Enhancers	Fetal Intestine Large	intestine
31	chr5:58446400-58446800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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