Variant report

Variant	rs16889512
Chromosome Location	chr5:58570068-58570069
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10038855	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10039990	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs10045441	0.84[ASN][1000 genomes]
rs10055869	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs10072367	1.00[CHB][hapmap]
rs13169097	1.00[CHB][hapmap]
rs13354612	0.84[ASN][1000 genomes]
rs154221	0.88[TSI][hapmap]
rs16889495	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889508	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17528543	0.87[CEU][hapmap];0.88[TSI][hapmap]
rs17528550	0.87[CEU][hapmap];0.88[TSI][hapmap]
rs2306292	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4618401	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9292199	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs9292200	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	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
3	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58561000-58571000	Weak transcription	Left Ventricle	heart
2	chr5:58565200-58571000	Weak transcription	Fetal Heart	heart
3	chr5:58567400-58572200	Active TSS	A549	lung
4	chr5:58567600-58570800	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr5:58568200-58572000	Active TSS	Colon Smooth Muscle	Colon
6	chr5:58568200-58572800	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr5:58568200-58572800	Active TSS	Stomach Smooth Muscle	stomach
8	chr5:58568400-58572000	Active TSS	Rectal Smooth Muscle	rectum
9	chr5:58568600-58570600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:58568600-58571600	Active TSS	Fetal Kidney	kidney
11	chr5:58568600-58572200	Active TSS	Fetal Muscle Trunk	muscle
12	chr5:58568600-58572400	Active TSS	Fetal Muscle Leg	muscle
13	chr5:58568600-58572600	Active TSS	Hela-S3	cervix
14	chr5:58568800-58571600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:58569000-58570200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr5:58569000-58572200	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr5:58569000-58572200	Active TSS	Fetal Intestine Large	intestine
18	chr5:58569200-58570200	Active TSS	HUVEC	blood vessel
19	chr5:58569200-58572200	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr5:58569200-58572400	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr5:58569400-58572200	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr5:58569600-58570200	Weak transcription	Brain Germinal Matrix	brain
23	chr5:58569800-58570400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr5:58569800-58570600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:58569800-58571000	Weak transcription	Fetal Brain Female	brain
26	chr5:58569800-58572200	Active TSS	Fetal Stomach	stomach
27	chr5:58570000-58570200	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr5:58570000-58570200	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr5:58570000-58570200	Flanking Active TSS	Fetal Intestine Small	intestine
30	chr5:58570000-58570200	Active TSS	Fetal Lung	lung
31	chr5:58570000-58570400	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr5:58570000-58570400	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr5:58570000-58571000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:58570000-58571200	Active TSS	Adipose Nuclei	Adipose
35	chr5:58570000-58571600	Active TSS	Psoas Muscle	Psoas
36	chr5:58570000-58572000	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr5:58570000-58572000	Active TSS	Brain Angular Gyrus	brain
38	chr5:58570000-58572000	Active TSS	Colonic Mucosa	Colon
39	chr5:58570000-58572200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:58570000-58572200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:58570000-58572400	Active TSS	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links