Variant report

Variant	rs30313
Chromosome Location	chr5:148157301-148157302
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10078593	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10078616	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10080209	0.85[AMR][1000 genomes]
rs10747517	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10747518	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875640	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11168059	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11168060	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11168061	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11168062	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11747905	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11750926	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12189260	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12517142	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12653443	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12654719	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1368279	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17108721	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs185021	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2082397	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2082398	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2163751	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2163752	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2400644	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2400645	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2400702	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2400703	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2400704	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs246502	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs246503	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs246504	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2568940	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2569000	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2569001	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2895774	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs30305	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs30306	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs30307	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30308	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30309	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30310	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs30311	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30314	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs30315	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs30316	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs30317	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs30318	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs30320	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs30321	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs30322	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs30323	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs30324	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs30325	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30326	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs30327	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs30328	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs30329	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs30330	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs30331	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3097815	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs39835	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs40949	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4429840	0.83[EUR][1000 genomes]
rs4513680	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4705058	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4705261	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4705262	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4705263	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4705265	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56043944	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56376672	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59386367	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59598688	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62388002	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6580579	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6580580	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6861953	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6865781	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6867058	0.88[EUR][1000 genomes]
rs6870415	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6870429	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6870766	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6874249	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6874997	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6879964	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6882470	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6882476	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6883606	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6885216	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6886359	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6892967	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7702609	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7737439	0.90[EUR][1000 genomes]
rs888953	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs888954	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs888955	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs919723	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs919724	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs30313	PLAC8L1	cis	parietal	SCAN
rs30313	PRELID2	cis	cerebellum	SCAN
rs30313	ZNF300	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:148149000-148158000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr5:148154000-148157800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:148154200-148158000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:148154200-148161400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr5:148155600-148157600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:148155600-148158200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:148155600-148158200	Enhancers	HMEC	breast
8	chr5:148155800-148157600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:148155800-148158000	Enhancers	Muscle Satellite Cultured Cells	--
10	chr5:148155800-148158200	Enhancers	NHEK	skin
11	chr5:148156000-148157400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:148156000-148157400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:148156000-148157400	Enhancers	Esophagus	oesophagus
14	chr5:148156200-148157400	Enhancers	Placenta Amnion	Placenta Amnion
15	chr5:148156400-148157400	Enhancers	NH-A	brain
16	chr5:148157000-148158400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr5:148157000-148158400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr5:148157200-148160800	Weak transcription	Gastric	stomach
19	chr5:148157200-148165800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:148157200-148170200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:148157200-148170600	Weak transcription	NHDF-Ad	bronchial

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