Variant report

Variant	rs957765
Chromosome Location	chr6:30142690-30142691
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1042338	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1076229	0.89[EUR][1000 genomes]
rs13194768	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419671	0.89[EUR][1000 genomes]
rs1419672	0.82[EUR][1000 genomes]
rs1419673	0.89[EUR][1000 genomes]
rs1541324	0.81[EUR][1000 genomes]
rs1573297	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1573298	0.81[EUR][1000 genomes]
rs1573299	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17194607	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2239530	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285796	0.84[EUR][1000 genomes]
rs2508030	0.84[EUR][1000 genomes]
rs2508031	0.82[EUR][1000 genomes]
rs2517606	0.88[ASN][1000 genomes]
rs2517616	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2517655	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2844775	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2857433	0.84[EUR][1000 genomes]
rs2857435	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2857438	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2857439	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2857440	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3778622	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3815079	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3815080	0.81[EUR][1000 genomes]
rs3815082	0.81[EUR][1000 genomes]
rs3815084	0.81[EUR][1000 genomes]
rs3815085	0.81[EUR][1000 genomes]
rs3815086	0.81[EUR][1000 genomes]
rs3888580	0.89[EUR][1000 genomes]
rs4392759	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4711211	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4713293	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4959011	0.81[EUR][1000 genomes]
rs4959012	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4959044	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs757259	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs757261	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs757262	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs757263	0.82[EUR][1000 genomes]
rs757264	0.81[EUR][1000 genomes]
rs7843	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261433	0.86[EUR][1000 genomes]
rs9261440	0.83[EUR][1000 genomes]
rs9261442	0.89[EUR][1000 genomes]
rs9261443	0.82[EUR][1000 genomes]
rs9261444	0.90[EUR][1000 genomes]
rs9261445	0.89[EUR][1000 genomes]
rs9261446	0.89[EUR][1000 genomes]
rs9261448	0.90[EUR][1000 genomes]
rs9261450	0.82[EUR][1000 genomes]
rs9261451	0.82[EUR][1000 genomes]
rs9261453	0.82[EUR][1000 genomes]
rs9261454	0.89[EUR][1000 genomes]
rs9261455	0.82[EUR][1000 genomes]
rs9261456	0.89[EUR][1000 genomes]
rs9261457	0.89[EUR][1000 genomes]
rs9261458	0.89[EUR][1000 genomes]
rs9261459	0.87[EUR][1000 genomes]
rs9261461	0.80[EUR][1000 genomes]
rs9261462	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261463	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261465	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261466	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9261467	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261468	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261470	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9261471	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261472	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9261473	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261479	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9261480	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9261481	0.81[EUR][1000 genomes]
rs9261482	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9261483	0.81[EUR][1000 genomes]
rs9261485	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9261486	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9261488	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261489	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261490	0.82[EUR][1000 genomes]
rs9261491	0.82[EUR][1000 genomes]
rs9261492	0.82[EUR][1000 genomes]
rs9261495	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261496	0.82[EUR][1000 genomes]
rs9261497	0.82[EUR][1000 genomes]
rs9261498	0.81[EUR][1000 genomes]
rs9261499	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261500	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261502	0.81[EUR][1000 genomes]
rs9261503	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261504	0.81[EUR][1000 genomes]
rs9261505	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261507	0.81[EUR][1000 genomes]
rs9261508	0.81[EUR][1000 genomes]
rs9261509	0.81[EUR][1000 genomes]
rs9261511	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261512	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9261513	0.81[EUR][1000 genomes]
rs9261514	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9261516	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9261517	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261518	0.82[EUR][1000 genomes]
rs9261519	0.82[EUR][1000 genomes]
rs9261521	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9261522	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9261523	0.82[EUR][1000 genomes]
rs9261524	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261525	0.82[EUR][1000 genomes]
rs9261526	0.84[EUR][1000 genomes]
rs9261527	0.82[EUR][1000 genomes]
rs9261528	0.82[EUR][1000 genomes]
rs9261529	0.83[EUR][1000 genomes]
rs9261530	0.84[EUR][1000 genomes]
rs9261531	0.84[EUR][1000 genomes]
rs9261532	0.84[EUR][1000 genomes]
rs9261533	0.86[EUR][1000 genomes]
rs9261535	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs929156	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9357094	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9380159	0.86[EUR][1000 genomes];0.91[ASN][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	nsv884057	chr6:30140540-30149251	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs957765	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs957765	HIST1H2BN	cis	parietal	SCAN
rs957765	HIST1H2AM	cis	parietal	SCAN
rs957765	BTN2A1	cis	cerebellum	SCAN
rs957765	ZKSCAN3	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30139000-30152000	Weak transcription	Liver	Liver
2	chr6:30141200-30146200	Weak transcription	HepG2	liver
3	chr6:30142000-30149200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:30142600-30142800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell

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