Variant report

Variant	rs12541491
Chromosome Location	chr8:10250048-10250049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11249992	0.84[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs11249995	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11249996	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11249999	0.88[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11250001	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11250002	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11779205	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11785061	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11989640	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12156350	0.85[CEU][hapmap]
rs12543645	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12544727	0.80[ASN][1000 genomes]
rs12547997	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12548025	0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12550717	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13254942	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13264580	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1986972	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2001337	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2001338	0.88[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3088186	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs34155841	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34381075	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34487437	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35060302	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35406700	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35472251	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35840352	0.90[EUR][1000 genomes]
rs4240645	0.96[CEU][hapmap];0.92[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4292737	0.85[EUR][1000 genomes]
rs4316191	0.86[EUR][1000 genomes]
rs4841329	0.84[CEU][hapmap]
rs6999466	0.81[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7460436	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7825778	0.81[CEU][hapmap]
rs7840461	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs9650650	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9657538	0.83[ASN][1000 genomes]
rs9657539	0.81[CHB][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv890347	chr8:10153082-10331636	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1022994	chr8:10190618-10660122	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv539466	chr8:10190618-10660122	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv527326	chr8:10199548-10320019	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1025557	chr8:10216726-10555187	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv465460	chr8:10241411-10290566	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
9	nsv610265	chr8:10241411-10290566	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12541491	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs12541491	BLK	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10192600-10282400	Weak transcription	Gastric	stomach
2	chr8:10224000-10255800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr8:10233800-10252400	Weak transcription	Fetal Brain Male	brain
4	chr8:10235200-10252400	Weak transcription	Brain Hippocampus Middle	brain
5	chr8:10235400-10256800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr8:10236200-10252600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr8:10236200-10255800	Weak transcription	Pancreas	Pancrea
8	chr8:10236200-10255800	Weak transcription	Right Ventricle	heart
9	chr8:10240400-10256000	Weak transcription	Adipose Nuclei	Adipose
10	chr8:10240400-10256800	Weak transcription	Left Ventricle	heart
11	chr8:10242000-10255800	Weak transcription	Brain Germinal Matrix	brain
12	chr8:10244800-10251200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr8:10245000-10253400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr8:10247800-10251000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr8:10248000-10250200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr8:10248000-10253200	Weak transcription	Spleen	Spleen
17	chr8:10248200-10252400	Weak transcription	HepG2	liver
18	chr8:10248200-10253200	Weak transcription	Liver	Liver
19	chr8:10248400-10255000	Weak transcription	Fetal Brain Female	brain
20	chr8:10249000-10250200	Enhancers	HSMMtube	muscle
21	chr8:10249000-10251200	Weak transcription	Primary T cells from cord blood	blood
22	chr8:10249000-10258200	Enhancers	Fetal Muscle Leg	muscle
23	chr8:10249000-10275200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr8:10249200-10250200	Enhancers	HSMM	muscle
25	chr8:10249600-10250200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr8:10249600-10250200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr8:10249600-10250200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr8:10249800-10251200	Enhancers	Fetal Muscle Trunk	muscle
29	chr8:10250000-10250200	Enhancers	NHLF	lung
30	chr8:10250000-10251800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr8:10250000-10252600	Weak transcription	NHDF-Ad	bronchial
32	chr8:10250000-10255400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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