Variant report

Variant	rs12543645
Chromosome Location	chr8:10246325-10246326
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	chr8:10240370..10243141-chr8:10246115..10249322,3	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11249992	0.84[CEU][hapmap];0.88[GIH][hapmap]
rs11249994	0.80[CHD][hapmap]
rs11249995	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11249996	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11249999	0.96[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11250001	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11250002	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1133184	0.93[CHD][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs11779205	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11785061	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11989640	0.96[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12156350	0.83[CEU][hapmap]
rs12541491	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12547997	0.90[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12548025	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12550717	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13254942	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13258627	0.83[CHB][hapmap]
rs13264580	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13272232	0.83[CHB][hapmap]
rs17151824	0.82[CHD][hapmap]
rs17767186	0.81[MEX][hapmap]
rs1986972	0.92[CEU][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2001337	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2001338	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3088186	0.80[CEU][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap]
rs34155841	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34381075	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34487437	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35060302	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35406700	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35472251	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35840352	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4240645	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4292737	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs4316191	0.82[EUR][1000 genomes]
rs4841329	0.87[CEU][hapmap]
rs6601455	0.83[CHB][hapmap]
rs6984231	0.84[CHD][hapmap]
rs6999466	0.88[CEU][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7015455	0.83[CHD][hapmap]
rs7460436	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7821526	0.83[CHB][hapmap]
rs9650650	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12543645	CLDN23	cis	multi-tissue	Pritchard
rs12543645	PPP1R3B	cis	cerebellum	SCAN
rs12543645	FLJ10661	cis	cerebellum	SCAN
rs12543645	BLK	Cis_chr	lymphoblastoid	RTeQTL
rs12543645	C8orf13	cis	multi-tissue	Pritchard
rs12543645	AGPAT5	cis	cerebellum	SCAN
rs12543645	DEFB136	cis	parietal	SCAN
rs12543645	MSRA	cis	parietal	SCAN
rs12543645	MFHAS1	cis	cerebellum	SCAN
rs12543645	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs12543645	FLJ10661	cis	parietal	SCAN

Chromatin state (count:24 , 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	chr8:10228600-10247800	Weak transcription	Liver	Liver
4	chr8:10233800-10252400	Weak transcription	Fetal Brain Male	brain
5	chr8:10235200-10252400	Weak transcription	Brain Hippocampus Middle	brain
6	chr8:10235400-10256800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr8:10236200-10247400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr8:10236200-10252600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr8:10236200-10255800	Weak transcription	Pancreas	Pancrea
10	chr8:10236200-10255800	Weak transcription	Right Ventricle	heart
11	chr8:10237200-10247400	Weak transcription	Lung	lung
12	chr8:10240400-10256000	Weak transcription	Adipose Nuclei	Adipose
13	chr8:10240400-10256800	Weak transcription	Left Ventricle	heart
14	chr8:10241200-10247400	Weak transcription	Spleen	Spleen
15	chr8:10241800-10246800	Weak transcription	Primary T cells from cord blood	blood
16	chr8:10241800-10249600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr8:10242000-10255800	Weak transcription	Brain Germinal Matrix	brain
18	chr8:10242200-10248200	Weak transcription	Fetal Brain Female	brain
19	chr8:10244800-10251200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr8:10245000-10247400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr8:10245000-10253400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr8:10246200-10246600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr8:10246200-10246800	Enhancers	Fetal Muscle Leg	muscle
24	chr8:10246200-10248000	Enhancers	Fetal Muscle Trunk	muscle

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