Variant report

Variant	rs9261448
Chromosome Location	chr6:30095329-30095330
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	chr6:30080946..30082589-chr6:30093243..30095341,2	MCF-7	breast:
2	chr6:30091019..30094481-chr6:30095201..30099363,3	K562	blood:

Extended variants
information (count: 132 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1042338	0.84[EUR][1000 genomes]
rs1076229	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947053	0.95[ASN][1000 genomes]
rs13194768	0.90[EUR][1000 genomes]
rs1419671	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1419672	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1419673	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1541324	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1573297	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1573298	0.88[EUR][1000 genomes]
rs1573299	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17194607	0.81[EUR][1000 genomes]
rs2239530	0.90[EUR][1000 genomes]
rs2284163	0.95[ASN][1000 genomes]
rs2285795	0.84[EUR][1000 genomes]
rs2285796	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2508030	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2508031	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2517653	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2517655	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28400887	0.88[ASN][1000 genomes]
rs2857433	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2857435	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2857438	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2857439	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2857440	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3778622	0.82[EUR][1000 genomes]
rs3815079	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3815080	0.88[EUR][1000 genomes]
rs3815082	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3815084	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3815085	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3815086	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3888580	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4392759	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4711211	0.82[EUR][1000 genomes]
rs4713293	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4959011	0.88[EUR][1000 genomes]
rs4959012	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4959041	0.95[ASN][1000 genomes]
rs4959044	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs757259	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs757261	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs757262	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs757263	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs757264	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7843	0.90[EUR][1000 genomes]
rs9261424	0.95[ASN][1000 genomes]
rs9261431	0.95[ASN][1000 genomes]
rs9261433	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9261438	0.95[ASN][1000 genomes]
rs9261439	0.95[ASN][1000 genomes]
rs9261440	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261442	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9261443	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261444	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9261445	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9261446	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9261449	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261450	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261451	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261453	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9261454	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261455	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9261456	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261457	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261458	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261459	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261461	0.90[EUR][1000 genomes]
rs9261462	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261463	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261465	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261466	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261467	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261468	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261470	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261471	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261472	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261473	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261479	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261480	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261481	0.89[EUR][1000 genomes]
rs9261482	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261483	0.88[EUR][1000 genomes]
rs9261484	0.86[EUR][1000 genomes]
rs9261485	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261486	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261488	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261489	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261490	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9261491	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9261492	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9261493	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261495	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261496	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9261497	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9261498	0.88[EUR][1000 genomes]
rs9261499	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261500	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261501	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9261502	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9261503	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261504	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261505	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261507	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9261508	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9261509	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9261511	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261512	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261513	0.88[EUR][1000 genomes]
rs9261514	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261516	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261517	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261518	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9261519	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9261521	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261522	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261523	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9261524	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261525	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9261526	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261527	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261528	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261529	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261530	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261531	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261532	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261533	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9261535	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs929156	0.82[EUR][1000 genomes]
rs957765	0.90[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9261448	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs9261448	BTN2A1	cis	cerebellum	SCAN
rs9261448	HIST1H2BN	cis	parietal	SCAN
rs9261448	HIST1H2AM	cis	parietal	SCAN
rs9261448	ZKSCAN3	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

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	chr6:30094600-30096000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:30094600-30096200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr6:30094800-30096000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr6:30094800-30096200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
8	chr6:30094800-30096200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr6:30094800-30096200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr6:30094800-30096200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:30095000-30095400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:30095000-30095400	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:30095000-30095400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:30095000-30095400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:30095000-30095600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:30095000-30095600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:30095000-30095600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
18	chr6:30095000-30095600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
19	chr6:30095000-30095600	Bivalent Enhancer	Spleen	Spleen
20	chr6:30095000-30095800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr6:30095000-30095800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:30095000-30095800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
23	chr6:30095000-30095800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:30095000-30095800	Bivalent Enhancer	Fetal Lung	lung
25	chr6:30095000-30095800	Enhancers	Pancreas	Pancrea
26	chr6:30095000-30096000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:30095000-30096000	Bivalent Enhancer	Left Ventricle	heart
28	chr6:30095000-30096200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:30095200-30095400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:30095200-30095400	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:30095200-30095400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:30095200-30095400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
33	chr6:30095200-30095400	Bivalent Enhancer	Fetal Intestine Large	intestine
34	chr6:30095200-30095400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
35	chr6:30095200-30095400	Active TSS	Right Ventricle	heart
36	chr6:30095200-30095400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
37	chr6:30095200-30095600	Bivalent Enhancer	Brain Anterior Caudate	brain
38	chr6:30095200-30095600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
39	chr6:30095200-30095600	Bivalent/Poised TSS	Fetal Brain Female	brain
40	chr6:30095200-30095600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
41	chr6:30095200-30095800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
42	chr6:30095200-30095800	Enhancers	Lung	lung
43	chr6:30095200-30095800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
44	chr6:30095200-30095800	Bivalent/Poised TSS	Psoas Muscle	Psoas
45	chr6:30095200-30095800	Active TSS	Right Atrium	heart
46	chr6:30095200-30095800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
47	chr6:30095200-30095800	Flanking Bivalent TSS/Enh	NHEK	skin
48	chr6:30095200-30096000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
49	chr6:30095200-30096000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr6:30095200-30096000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin

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