Variant report

Variant	rs10070294
Chromosome Location	chr5:58564996-58564997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10036406	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs10038599	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10055446	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs10059709	0.88[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap]
rs10061600	0.83[ASN][1000 genomes]
rs10061786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10064893	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs10068836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10070436	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs10075364	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10440630	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs11740402	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11747413	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs13328160	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs13328175	0.83[CEU][hapmap];0.95[EUR][1000 genomes]
rs13328226	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13354210	0.84[CEU][hapmap]
rs13360907	0.98[ASN][1000 genomes]
rs17444059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17528257	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17528285	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs17528473	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17528634	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs17780213	0.81[CEU][hapmap]
rs17780740	0.83[CEU][hapmap]
rs2112959	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28529077	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28647633	0.98[ASN][1000 genomes]
rs60453299	0.98[ASN][1000 genomes]
rs61683381	0.91[EUR][1000 genomes]
rs6881054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765932	0.87[ASN][1000 genomes]
rs72765942	0.98[ASN][1000 genomes]
rs72765953	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765961	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765990	0.91[EUR][1000 genomes]
rs9292201	0.84[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs9686434	0.91[EUR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10070294	PLK2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58553800-58568600	Weak transcription	Fetal Muscle Leg	muscle
2	chr5:58560200-58566600	Enhancers	Rectal Smooth Muscle	rectum
3	chr5:58560400-58570000	Weak transcription	Fetal Lung	lung
4	chr5:58561000-58569800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:58561000-58571000	Weak transcription	Left Ventricle	heart
6	chr5:58562000-58565400	Enhancers	Colon Smooth Muscle	Colon
7	chr5:58562800-58568800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:58563000-58568200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:58563000-58568200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:58563000-58568800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr5:58563000-58569000	Weak transcription	Psoas Muscle	Psoas
12	chr5:58563200-58566400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:58563600-58566800	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr5:58563800-58568600	Weak transcription	Fetal Intestine Large	intestine
15	chr5:58564400-58565000	Weak transcription	Fetal Heart	heart
16	chr5:58564400-58565400	Enhancers	Hela-S3	cervix
17	chr5:58564600-58567400	Transcr. at gene 5' and 3'	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links