Variant report

Variant	rs4959041
Chromosome Location	chr6:30077967-30077968
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	chr6:30073473..30076763-chr6:30077230..30080756,3	K562	blood:

Variant related genes	Relation type
ENSG00000204616	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1076229	0.97[ASN][1000 genomes]
rs10947053	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419671	0.97[ASN][1000 genomes]
rs1419672	0.91[ASN][1000 genomes]
rs1419673	0.99[ASN][1000 genomes]
rs1541324	0.87[ASN][1000 genomes]
rs1573297	0.92[ASN][1000 genomes]
rs1573298	0.82[ASN][1000 genomes]
rs1573299	0.92[ASN][1000 genomes]
rs2284163	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285796	0.86[ASN][1000 genomes]
rs2508030	0.86[ASN][1000 genomes]
rs2508031	0.84[ASN][1000 genomes]
rs2517653	0.83[ASN][1000 genomes]
rs2517655	0.89[ASN][1000 genomes]
rs28400887	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2857433	0.86[ASN][1000 genomes]
rs2857435	0.88[ASN][1000 genomes]
rs2857436	0.82[ASN][1000 genomes]
rs2857438	0.88[ASN][1000 genomes]
rs2857439	0.92[ASN][1000 genomes]
rs2857440	0.88[ASN][1000 genomes]
rs2857458	0.82[ASN][1000 genomes]
rs3815079	0.90[ASN][1000 genomes]
rs3815080	0.82[ASN][1000 genomes]
rs3815082	0.87[ASN][1000 genomes]
rs3815084	0.87[ASN][1000 genomes]
rs3815085	0.87[ASN][1000 genomes]
rs3815086	0.87[ASN][1000 genomes]
rs3888580	0.97[ASN][1000 genomes]
rs4392759	0.92[ASN][1000 genomes]
rs4713293	0.85[ASN][1000 genomes]
rs4959011	0.82[ASN][1000 genomes]
rs4959012	0.92[ASN][1000 genomes]
rs4959044	0.92[ASN][1000 genomes]
rs757259	0.92[ASN][1000 genomes]
rs757261	0.92[ASN][1000 genomes]
rs757262	0.92[ASN][1000 genomes]
rs757263	0.94[ASN][1000 genomes]
rs757264	0.94[ASN][1000 genomes]
rs9261424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261431	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261433	0.99[ASN][1000 genomes]
rs9261438	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261439	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261440	0.96[ASN][1000 genomes]
rs9261442	0.99[ASN][1000 genomes]
rs9261443	0.91[ASN][1000 genomes]
rs9261444	0.99[ASN][1000 genomes]
rs9261445	0.99[ASN][1000 genomes]
rs9261446	0.99[ASN][1000 genomes]
rs9261448	0.95[ASN][1000 genomes]
rs9261449	0.97[ASN][1000 genomes]
rs9261450	0.94[ASN][1000 genomes]
rs9261451	0.94[ASN][1000 genomes]
rs9261453	0.93[ASN][1000 genomes]
rs9261454	0.96[ASN][1000 genomes]
rs9261455	0.93[ASN][1000 genomes]
rs9261456	0.96[ASN][1000 genomes]
rs9261457	0.96[ASN][1000 genomes]
rs9261458	0.96[ASN][1000 genomes]
rs9261459	0.96[ASN][1000 genomes]
rs9261461	0.82[ASN][1000 genomes]
rs9261462	0.92[ASN][1000 genomes]
rs9261463	0.92[ASN][1000 genomes]
rs9261465	0.92[ASN][1000 genomes]
rs9261466	0.88[ASN][1000 genomes]
rs9261467	0.92[ASN][1000 genomes]
rs9261468	0.92[ASN][1000 genomes]
rs9261470	0.88[ASN][1000 genomes]
rs9261471	0.92[ASN][1000 genomes]
rs9261472	0.88[ASN][1000 genomes]
rs9261473	0.92[ASN][1000 genomes]
rs9261479	0.86[ASN][1000 genomes]
rs9261480	0.86[ASN][1000 genomes]
rs9261481	0.82[ASN][1000 genomes]
rs9261482	0.88[ASN][1000 genomes]
rs9261483	0.82[ASN][1000 genomes]
rs9261484	0.82[ASN][1000 genomes]
rs9261485	0.88[ASN][1000 genomes]
rs9261486	0.88[ASN][1000 genomes]
rs9261488	0.92[ASN][1000 genomes]
rs9261489	0.92[ASN][1000 genomes]
rs9261490	0.87[ASN][1000 genomes]
rs9261491	0.87[ASN][1000 genomes]
rs9261492	0.87[ASN][1000 genomes]
rs9261493	0.84[ASN][1000 genomes]
rs9261495	0.92[ASN][1000 genomes]
rs9261496	0.87[ASN][1000 genomes]
rs9261497	0.87[ASN][1000 genomes]
rs9261498	0.82[ASN][1000 genomes]
rs9261499	0.92[ASN][1000 genomes]
rs9261500	0.92[ASN][1000 genomes]
rs9261501	0.87[ASN][1000 genomes]
rs9261502	0.87[ASN][1000 genomes]
rs9261503	0.92[ASN][1000 genomes]
rs9261504	0.88[ASN][1000 genomes]
rs9261505	0.92[ASN][1000 genomes]
rs9261507	0.87[ASN][1000 genomes]
rs9261508	0.87[ASN][1000 genomes]
rs9261509	0.87[ASN][1000 genomes]
rs9261511	0.92[ASN][1000 genomes]
rs9261512	0.89[ASN][1000 genomes]
rs9261513	0.82[ASN][1000 genomes]
rs9261514	0.91[ASN][1000 genomes]
rs9261516	0.89[ASN][1000 genomes]
rs9261517	0.92[ASN][1000 genomes]
rs9261518	0.87[ASN][1000 genomes]
rs9261519	0.87[ASN][1000 genomes]
rs9261521	0.89[ASN][1000 genomes]
rs9261522	0.89[ASN][1000 genomes]
rs9261523	0.87[ASN][1000 genomes]
rs9261524	0.92[ASN][1000 genomes]
rs9261525	0.87[ASN][1000 genomes]
rs9261526	0.86[ASN][1000 genomes]
rs9261527	0.84[ASN][1000 genomes]
rs9261528	0.84[ASN][1000 genomes]
rs9261529	0.86[ASN][1000 genomes]
rs9261530	0.86[ASN][1000 genomes]
rs9261531	0.86[ASN][1000 genomes]
rs9261532	0.86[ASN][1000 genomes]
rs9261533	0.86[ASN][1000 genomes]
rs9261535	0.84[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	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs4959041	HLA-H	cis	lymphoblastoid	seeQTL
rs4959041	NDUFS1	trans	multi-tissue	Pritchard
rs4959041	HLA-F	cis	multi-tissue	Pritchard
rs4959041	TPD52L2	trans	multi-tissue	Pritchard
rs4959041	ZKSCAN3	cis	cerebellum	SCAN
rs4959041	TFG	trans	multi-tissue	Pritchard
rs4959041	HIST1H2AH	cis	cerebellum	SCAN
rs4959041	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs4959041	HIST1H2AI	cis	parietal	SCAN
rs4959041	HLA-G	cis	multi-tissue	Pritchard
rs4959041	HIST1H2AM	cis	parietal	SCAN
rs4959041	KIT	trans	multi-tissue	Pritchard
rs4959041	HLA-H	cis	multi-tissue	Pritchard
rs4959041	BTN2A1	cis	cerebellum	SCAN
rs4959041	HCG4	cis	multi-tissue	Pritchard
rs4959041	HLA-A	cis	multi-tissue	Pritchard
rs4959041	HCG4P6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30071600-30079200	Weak transcription	Gastric	stomach
2	chr6:30072200-30078000	Weak transcription	Colonic Mucosa	Colon
3	chr6:30075800-30078000	Weak transcription	Fetal Intestine Small	intestine
4	chr6:30076000-30079400	Weak transcription	Hela-S3	cervix
5	chr6:30077200-30078200	Weak transcription	Stomach Mucosa	stomach

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