Variant report

Variant	rs12546285
Chromosome Location	chr8:126085586-126085587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:126080766..126090501-chr8:126099504..126106488,12	MCF-7	breast:
2	chr8:126084798..126089198-chr8:126089472..126091426,4	MCF-7	breast:
3	chr8:126083918..126086444-chr8:126443181..126445574,2	MCF-7	breast:
4	chr8:126073739..126076333-chr8:126082992..126086682,3	K562	blood:

Variant related genes	Relation type
ENSG00000164961	Chromatin interaction
ENSG00000173334	Chromatin interaction
ENSG00000156831	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10086228	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10092712	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10095967	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10096319	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10097947	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10104486	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10107270	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10111425	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1019705	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10441518	0.81[AMR][1000 genomes]
rs12542195	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12545710	0.82[AMR][1000 genomes]
rs12676128	0.87[ASN][1000 genomes]
rs13248796	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13263702	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13264301	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13282919	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2217132	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2288310	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2288312	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2303522	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303525	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2384915	0.82[AMR][1000 genomes]
rs2384921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28670937	0.81[AMR][1000 genomes]
rs28716650	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34818959	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3793447	0.81[AMR][1000 genomes]
rs4871568	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6470326	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6651230	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6989556	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6991343	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7003069	0.82[AMR][1000 genomes]
rs7357375	0.87[EUR][1000 genomes]
rs7832609	0.85[AMR][1000 genomes]
rs9297709	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs966945	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891434	chr8:125630655-126324432	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1030748	chr8:126012282-126137840	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv539743	chr8:126012282-126137840	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv949614	chr8:126063646-126376699	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv465803	chr8:126068197-126132816	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
6	nsv612148	chr8:126068197-126132816	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12546285	SQLE	cis	brain	BrainEAC

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:126015400-126098000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr8:126023600-126099000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr8:126028600-126097400	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr8:126029800-126097400	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr8:126029800-126103000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr8:126038800-126097200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr8:126039400-126091400	Strong transcription	Duodenum Smooth Muscle	Duodenum
8	chr8:126042400-126096800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr8:126042600-126098600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr8:126042600-126098800	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr8:126043000-126096000	Strong transcription	Liver	Liver
12	chr8:126043000-126098000	Strong transcription	Fetal Thymus	thymus
13	chr8:126045600-126095000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr8:126046600-126099600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr8:126046800-126096200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr8:126050200-126089000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:126052800-126103200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr8:126055800-126088600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr8:126064200-126102800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr8:126066600-126099400	Strong transcription	Primary B cells from cord blood	blood
21	chr8:126071800-126103000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr8:126072200-126085600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr8:126072800-126095600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr8:126073000-126095200	Strong transcription	Adipose Nuclei	Adipose
25	chr8:126073000-126095800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr8:126073200-126086200	Strong transcription	Fetal Muscle Leg	muscle
27	chr8:126073200-126087400	Strong transcription	Brain Cingulate Gyrus	brain
28	chr8:126073200-126095000	Strong transcription	Stomach Smooth Muscle	stomach
29	chr8:126073200-126095600	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr8:126073200-126098200	Strong transcription	Primary hematopoietic stem cells	blood
31	chr8:126073200-126098400	Strong transcription	Primary T cells from cord blood	blood
32	chr8:126073400-126095600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr8:126073400-126096400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr8:126073600-126085600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr8:126073600-126086400	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr8:126073600-126095600	Strong transcription	Fetal Lung	lung
37	chr8:126073800-126087200	Strong transcription	Brain Substantia Nigra	brain
38	chr8:126074200-126087000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr8:126075400-126085600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr8:126075400-126087800	Strong transcription	Brain Anterior Caudate	brain
41	chr8:126076000-126085600	Strong transcription	Fetal Stomach	stomach
42	chr8:126076800-126095800	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr8:126077200-126085600	Strong transcription	Brain Germinal Matrix	brain
44	chr8:126077200-126095600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr8:126077600-126087000	Strong transcription	Brain Angular Gyrus	brain
46	chr8:126078000-126088400	Strong transcription	Brain Hippocampus Middle	brain
47	chr8:126078200-126087600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr8:126078400-126085600	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr8:126078400-126096000	Strong transcription	Dnd41	blood
50	chr8:126078600-126085600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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