Variant report

Variant	rs246503
Chromosome Location	chr5:148171714-148171715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10078593	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10078616	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10080209	0.88[ASN][1000 genomes]
rs10747517	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10747518	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10875640	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168059	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168060	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168061	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168062	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11747905	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11750926	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12189260	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12517142	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12653443	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12654719	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1368279	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17108721	0.82[ASN][1000 genomes]
rs185021	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2082397	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2082398	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2163751	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2163752	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2400644	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2400702	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2400703	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2400704	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs246502	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs246504	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568940	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2569000	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2569001	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2895774	0.81[ASN][1000 genomes]
rs30305	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs30306	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs30307	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs30308	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs30309	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs30310	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs30311	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs30312	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs30313	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs30314	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs30315	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs30316	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs30317	0.84[ASN][1000 genomes]
rs30318	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs30320	0.88[EUR][1000 genomes]
rs30321	0.88[EUR][1000 genomes]
rs30322	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs30323	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs30324	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs30325	0.80[EUR][1000 genomes]
rs30326	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs30327	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs30328	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs30329	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs30330	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs30331	0.82[EUR][1000 genomes]
rs3097815	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs39835	0.83[ASN][1000 genomes]
rs40949	0.83[ASN][1000 genomes]
rs4429840	0.87[ASN][1000 genomes]
rs4513680	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4705261	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4705262	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4705263	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4705265	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56043944	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56376672	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59386367	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59598688	0.81[ASN][1000 genomes]
rs62388002	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6580579	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6580580	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6861953	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6865781	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6867058	0.91[ASN][1000 genomes]
rs6870415	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6870429	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6870766	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6874249	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6879964	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6882470	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6882476	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6883606	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6885216	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6886359	0.81[ASN][1000 genomes]
rs6892967	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7702609	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7737439	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs919723	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs919724	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv883021	chr5:148060817-148182123	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv462481	chr5:148130138-148172689	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv599946	chr5:148130138-148172689	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs246503	SPINK14	cis	cerebellum	SCAN
rs246503	PRELID2	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:148168000-148171800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:148168800-148172400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:148170000-148171800	Enhancers	Osteobl	bone
4	chr5:148170000-148175600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr5:148170200-148171800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:148170200-148173400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:148170200-148174800	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr5:148170400-148173400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:148170400-148175800	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr5:148170800-148173600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:148170800-148175200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr5:148170800-148175400	Enhancers	GM12878-XiMat	blood
13	chr5:148171000-148172000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:148171000-148173400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:148171000-148173400	Enhancers	HMEC	breast
16	chr5:148171400-148171800	Enhancers	Left Ventricle	heart
17	chr5:148171400-148172600	Weak transcription	NH-A	brain
18	chr5:148171400-148172800	Weak transcription	HSMM	muscle
19	chr5:148171600-148172000	Enhancers	NHEK	skin
20	chr5:148171600-148172600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:148171600-148172600	Weak transcription	NHDF-Ad	bronchial
22	chr5:148171600-148173000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:148171600-148173200	Weak transcription	Esophagus	oesophagus
24	chr5:148171600-148176200	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links