Variant report

Variant	rs9261431
Chromosome Location	chr6:30086422-30086423
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30083851..30086480-chr6:30123012..30125789,2	MCF-7	breast:
2	chr6:30079728..30082386-chr6:30085707..30087606,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204616	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1076229	0.97[ASN][1000 genomes]
rs10947053	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	0.93[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]
rs4959041	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	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	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261439	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[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:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv884055	chr6:30078275-30087776	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv601476	chr6:30085838-30091311	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9261431	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs9261431	HCG4P6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30082000-30089400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr6:30082200-30087400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:30082400-30087200	Weak transcription	Hela-S3	cervix
4	chr6:30082400-30091000	Weak transcription	HepG2	liver
5	chr6:30086000-30086800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:30086200-30088000	Enhancers	Fetal Intestine Large	intestine
7	chr6:30086200-30092600	Enhancers	Fetal Intestine Small	intestine
8	chr6:30086400-30087600	Enhancers	Stomach Mucosa	stomach
9	chr6:30086400-30087600	Enhancers	A549	lung
10	chr6:30086400-30088000	Enhancers	Rectal Mucosa Donor 31	rectum

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