Variant report

Variant	rs9261445
Chromosome Location	chr6:30094788-30094789
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30080946..30082589-chr6:30093243..30095341,2	MCF-7	breast:
2	chr6:30093045..30094849-chr6:30097589..30099576,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM31-2	chr6:30093187-30095185	NONHSAT108603

Extended variants
information (count: 134 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs1042338	0.83[EUR][1000 genomes]
rs1076229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10947053	0.99[ASN][1000 genomes]
rs13194768	0.89[EUR][1000 genomes]
rs1419671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1419672	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1419673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541324	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1573297	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1573298	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1573299	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17194607	0.80[EUR][1000 genomes]
rs2239530	0.89[EUR][1000 genomes]
rs2284163	0.99[ASN][1000 genomes]
rs2285795	0.85[EUR][1000 genomes]
rs2285796	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2508030	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2508031	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2517653	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2517655	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28400887	0.92[ASN][1000 genomes]
rs2857433	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2857435	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2857436	0.83[ASN][1000 genomes]
rs2857438	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2857439	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2857440	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2857458	0.83[ASN][1000 genomes]
rs3778622	0.81[EUR][1000 genomes]
rs3815079	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3815080	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3815082	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3815084	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3815085	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3815086	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3888580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4392759	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4711211	0.81[EUR][1000 genomes]
rs4713293	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4959011	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4959012	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4959041	0.99[ASN][1000 genomes]
rs4959044	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs757259	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs757261	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs757262	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs757263	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs757264	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7843	0.89[EUR][1000 genomes]
rs9261424	0.99[ASN][1000 genomes]
rs9261431	0.99[ASN][1000 genomes]
rs9261433	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261438	0.99[ASN][1000 genomes]
rs9261439	0.99[ASN][1000 genomes]
rs9261440	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261443	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9261444	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261448	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9261449	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9261450	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261451	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261453	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261454	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261455	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261456	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261457	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261458	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261459	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261461	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261462	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261463	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261465	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261466	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261467	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261468	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261470	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261471	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261472	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261473	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261479	0.87[AFR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261480	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261481	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261482	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261483	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261484	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261485	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261486	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261488	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261489	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261490	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261491	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261492	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261493	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261495	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261496	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261497	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261498	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261499	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261500	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261501	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261502	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261503	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261504	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261505	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261507	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261508	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261509	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261511	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261512	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9261513	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261514	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9261516	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9261517	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261518	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261519	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261521	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9261522	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9261523	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261524	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261525	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261526	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261527	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261528	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261529	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261530	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261531	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261532	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261533	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261535	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs929156	0.82[EUR][1000 genomes]
rs957765	0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv884056	chr6:30089623-30097818	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9261445	HLA-A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30092400-30096200	Weak transcription	Hela-S3	cervix
2	chr6:30092600-30097200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:30094400-30096000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:30094600-30094800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
5	chr6:30094600-30096000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:30094600-30096200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell

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