Variant report

Variant	rs12543308
Chromosome Location	chr8:11308793-11308794
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:11299743..11301452-chr8:11307305..11309157,2	MCF-7	breast:
2	chr8:11302281..11304397-chr8:11308190..11310452,3	K562	blood:
3	chr8:11306364..11309144-chr8:11311400..11314118,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154319	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10088323	0.86[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs10448145	0.81[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10481455	0.81[JPT][hapmap]
rs10503423	0.81[CHB][hapmap]
rs1057750	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs10903338	0.93[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11250136	0.96[ASN][1000 genomes]
rs11250137	0.95[ASN][1000 genomes]
rs11250138	0.86[CHB][hapmap]
rs11777505	0.88[ASN][1000 genomes]
rs11779875	0.86[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs11782375	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs11785710	0.85[ASN][1000 genomes]
rs11991448	0.92[ASN][1000 genomes]
rs11991453	0.95[ASN][1000 genomes]
rs12114115	0.85[CEU][hapmap];0.81[CHD][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs12549796	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs13248746	0.94[ASN][1000 genomes]
rs13251015	0.82[EUR][1000 genomes]
rs13253092	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs13259219	0.81[CHB][hapmap]
rs13264212	1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs13439411	0.91[CHB][hapmap];0.91[CHD][hapmap];0.80[ASN][1000 genomes]
rs2003422	0.87[ASN][1000 genomes]
rs2003423	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2280803	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2409766	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2409767	0.91[ASN][1000 genomes]
rs2409770	0.90[ASN][1000 genomes]
rs2409771	0.91[ASN][1000 genomes]
rs2409772	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2409773	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2409774	0.98[ASN][1000 genomes]
rs2409775	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2618431	0.86[CHB][hapmap]
rs2618475	0.81[CHB][hapmap]
rs2736320	0.82[CHB][hapmap]
rs28700987	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2898279	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2898280	0.91[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs34013904	0.81[ASN][1000 genomes]
rs35161715	0.95[ASN][1000 genomes]
rs35433745	0.87[ASN][1000 genomes]
rs3989103	0.95[ASN][1000 genomes]
rs4240675	0.84[CEU][hapmap];0.81[CHB][hapmap];0.88[EUR][1000 genomes]
rs4581006	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs4840560	0.98[ASN][1000 genomes]
rs4840561	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4840562	0.81[ASN][1000 genomes]
rs4841529	0.81[JPT][hapmap]
rs4841530	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs4841533	0.97[ASN][1000 genomes]
rs4841534	0.98[ASN][1000 genomes]
rs4841535	0.97[ASN][1000 genomes]
rs4841536	0.98[ASN][1000 genomes]
rs4841537	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4841539	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4841540	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4841542	0.83[ASN][1000 genomes]
rs58004460	0.92[ASN][1000 genomes]
rs6601589	0.95[ASN][1000 genomes]
rs6601592	0.81[CHB][hapmap]
rs6982606	0.85[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs6983820	0.97[ASN][1000 genomes]
rs6984212	0.85[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs6998387	0.86[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs7001675	0.86[CHB][hapmap]
rs7007712	0.82[CHB][hapmap]
rs7018402	0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs7830445	0.88[ASN][1000 genomes]
rs7846252	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs9644687	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs9693089	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs9792166	0.95[ASN][1000 genomes]
rs9792175	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9792227	0.86[ASN][1000 genomes]
rs9792375	0.86[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs9792397	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1022525	chr8:11066191-11309356	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv539474	chr8:11066191-11309356	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv34097	chr8:11177372-11489894	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv522860	chr8:11253879-11330364	Bivalent/Poised TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv890357	chr8:11286146-11330364	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1030756	chr8:11292073-11332782	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1022074	chr8:11292256-11394526	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12543308	CTSB	cis	cerebellum	SCAN
rs12543308	C8orf79	cis	cerebellum	SCAN
rs12543308	TDH	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11280600-11308800	Weak transcription	Primary B cells from cord blood	blood
2	chr8:11287800-11313600	Weak transcription	Right Atrium	heart
3	chr8:11292400-11313000	Weak transcription	Pancreas	Pancrea
4	chr8:11296200-11319200	Enhancers	Fetal Thymus	thymus
5	chr8:11303600-11323200	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr8:11305800-11310600	Enhancers	Brain Substantia Nigra	brain
7	chr8:11305800-11312200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:11306000-11310400	Enhancers	Brain Angular Gyrus	brain
9	chr8:11306000-11310400	Enhancers	Brain Cingulate Gyrus	brain
10	chr8:11306000-11310400	Enhancers	Brain Hippocampus Middle	brain
11	chr8:11306400-11311800	Weak transcription	Gastric	stomach
12	chr8:11306400-11312200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr8:11306600-11311400	Weak transcription	A549	lung
14	chr8:11306800-11308800	Weak transcription	Spleen	Spleen
15	chr8:11306800-11310400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr8:11307000-11311400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr8:11307000-11311400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr8:11307200-11314000	Weak transcription	Fetal Heart	heart
19	chr8:11307200-11322000	Weak transcription	HSMMtube	muscle
20	chr8:11307400-11309600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr8:11307400-11309800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr8:11307400-11312000	Weak transcription	Esophagus	oesophagus
23	chr8:11307600-11310600	Enhancers	Brain Anterior Caudate	brain
24	chr8:11307600-11312400	Weak transcription	Right Ventricle	heart
25	chr8:11307600-11319800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr8:11307800-11308800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr8:11307800-11311600	Weak transcription	Fetal Brain Male	brain
28	chr8:11307800-11313800	Weak transcription	NHEK	skin
29	chr8:11308000-11309000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr8:11308000-11312000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr8:11308200-11311600	Weak transcription	Fetal Brain Female	brain
32	chr8:11308200-11313200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr8:11308200-11313400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr8:11308400-11314600	Enhancers	Thymus	Thymus
35	chr8:11308600-11308800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr8:11308600-11309600	Enhancers	GM12878-XiMat	blood
37	chr8:11308600-11310600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr8:11308600-11314000	Enhancers	Primary T cells fromperipheralblood	blood
39	chr8:11308600-11314800	Enhancers	Primary B cells from peripheral blood	blood

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