Variant report

Variant	rs9321999
Chromosome Location	chr6:145209853-145209854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:145202232..145204712-chr6:145207955..145210367,2	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs12175408	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12175421	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13195749	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13198108	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13201654	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13210889	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13216871	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs13217690	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1338696	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1338697	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1538401	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1538402	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2153108	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2153109	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2153110	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2185143	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35285375	0.91[ASN][1000 genomes]
rs35361162	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35946718	0.92[ASN][1000 genomes]
rs4143178	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4331996	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4331997	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4526219	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4637659	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4895660	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4896761	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4896762	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57590687	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62438853	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6570657	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570659	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6570660	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6570661	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6909971	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6910398	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6914560	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6930238	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6931199	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6934724	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6935054	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6935093	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6935178	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6935436	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7742815	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7742893	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7743204	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7762951	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9283117	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9285505	0.80[ASN][1000 genomes]
rs9321998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9322000	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9322001	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9322002	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9322003	0.80[ASN][1000 genomes]
rs9322004	0.80[ASN][1000 genomes]
rs9376873	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9376877	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9386088	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9390249	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390250	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9399516	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9399517	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9403622	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9403624	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9403625	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9403626	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9403627	0.80[ASN][1000 genomes]
rs9403630	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9497118	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9497128	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9688347	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9688355	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9688729	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv464070	chr6:145184504-145214952	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv604823	chr6:145184504-145214952	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv1850377	chr6:145199259-145319640	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9321999	PLAGL1	cis	cerebellum	SCAN
rs9321999	VTA1	cis	cerebellum	SCAN
rs9321999	VTA1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145209800-145210200	Enhancers	HSMM	muscle

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