Variant report

Variant	rs13043266
Chromosome Location	chr20:23588127-23588128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr20:23588020-23588170	NB4	blood:	n/a	n/a
2	CTCF	chr20:23586943-23588211	A549	lung:	n/a	chr20:23587368-23587389 chr20:23587109-23587122 chr20:23587373-23587391 chr20:23587070-23587078
3	CTCF	chr20:23588000-23588150	GM12873	blood:	n/a	n/a
4	RAD21	chr20:23587152-23588127	SK-N-SH	brain:	n/a	chr20:23587214-23587227 chr20:23587213-23587225 chr20:23587371-23587390

No.	Distal block	Cell Line	Cell type
1	chr20:23330189..23333651-chr20:23586751..23589419,5	MCF-7	breast:
2	chr20:23426997..23427916-chr20:23586801..23588394,7	MCF-7	breast:
3	chr20:23587750..23589396-chr20:23593301..23594908,2	MCF-7	breast:

Variant related genes	Relation type
CST9	TF binding region
ENSG00000234832	Chromatin interaction
ENSG00000132661	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1010117	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1011226	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1064039	0.85[EUR][1000 genomes]
rs1158167	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12624424	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12625182	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12625716	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12710327	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13037490	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13038305	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13038337	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13038990	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13039536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13040663	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13041070	0.87[EUR][1000 genomes]
rs13043610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1555355	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17751897	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2016161	0.85[EUR][1000 genomes]
rs2067488	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2208289	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2254635	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2405367	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs2405392	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2405393	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2424582	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs28703706	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3004139	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3004145	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3088162	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34374560	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34746357	0.85[EUR][1000 genomes]
rs34792920	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34897231	0.85[EUR][1000 genomes]
rs34911568	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35488434	0.85[EUR][1000 genomes]
rs35573837	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35610040	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs35782710	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35966482	0.85[EUR][1000 genomes]
rs3761280	0.85[EUR][1000 genomes]
rs3761281	0.85[EUR][1000 genomes]
rs3787498	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs3787499	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs3810575	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3827141	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs3827142	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs3827143	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4346460	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4815222	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4815223	0.94[CEU][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4815224	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5030707	0.85[EUR][1000 genomes]
rs55897275	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56077567	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56371840	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56388902	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57549987	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59059917	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6036461	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6036463	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036465	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6036469	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6036470	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6036471	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6036474	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6036476	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6036478	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6048920	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048922	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6048923	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6048924	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6048925	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6048926	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6048928	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6048929	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6048930	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6048933	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048936	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6048937	0.85[ASN][1000 genomes]
rs6048939	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048941	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048945	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6048946	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6048949	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6048950	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6048952	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048956	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61035931	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6106685	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6114201	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6114206	0.84[EUR][1000 genomes]
rs6114208	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs6114209	0.85[EUR][1000 genomes]
rs6515375	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67567111	0.85[EUR][1000 genomes]
rs67997662	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71334202	0.81[EUR][1000 genomes]
rs7265178	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7270413	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73318135	0.84[EUR][1000 genomes]
rs734801	0.82[EUR][1000 genomes]
rs8114619	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8115417	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8115423	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8116859	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8121147	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8121283	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8121405	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs911119	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[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	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13043266	CST3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23583400-23594000	Weak transcription	Right Atrium	heart
2	chr20:23585000-23588800	Enhancers	Fetal Thymus	thymus
3	chr20:23586000-23588600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr20:23586600-23590000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr20:23586800-23589000	Enhancers	HepG2	liver
6	chr20:23587000-23588200	Enhancers	Esophagus	oesophagus
7	chr20:23587000-23595600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr20:23587200-23588200	Enhancers	Brain Substantia Nigra	brain
9	chr20:23587200-23588200	Enhancers	GM12878-XiMat	blood
10	chr20:23587200-23589200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr20:23587200-23590400	Enhancers	Brain Anterior Caudate	brain
12	chr20:23587400-23588200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr20:23587400-23588200	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr20:23587400-23588400	Enhancers	Brain Hippocampus Middle	brain
15	chr20:23587600-23588200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr20:23587800-23588200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr20:23587800-23589000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr20:23587800-23589000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr20:23587800-23589800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr20:23587800-23589800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr20:23587800-23590400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr20:23587800-23594000	Weak transcription	Colon Smooth Muscle	Colon

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