Variant report

Variant	rs7270413
Chromosome Location	chr20:23593821-23593822
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23593307..23595143-chr20:23609634..23612477,2	K562	blood:
2	chr20:23593520..23595172-chr20:23617829..23619387,2	MCF-7	breast:
3	chr20:23587750..23589396-chr20:23593301..23594908,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101439	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1010117	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1011226	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1064039	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1158167	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12624424	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12625182	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12625716	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12710327	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13037490	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13038305	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13038337	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13038990	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13039536	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13040663	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13041070	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13043266	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13043610	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1555355	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17751897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016161	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2067488	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2208289	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2405392	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2405393	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2424582	0.82[ASN][1000 genomes]
rs28703706	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3004139	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3004145	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3088162	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34374560	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34746357	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34792920	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34897231	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34911568	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35488434	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35573837	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35610040	0.84[EUR][1000 genomes]
rs35782710	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35966482	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3761280	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3761281	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3787498	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3787499	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3810575	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3827141	0.84[EUR][1000 genomes]
rs3827142	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3827143	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4346460	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4815222	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4815223	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4815224	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5030707	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55897275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56077567	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56371840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56388902	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57549987	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59059917	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036461	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6036463	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6036465	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6036469	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6036470	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036471	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036474	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6036476	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036478	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048920	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048922	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048923	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048924	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048925	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048926	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048928	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6048929	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6048933	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048936	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6048937	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6048939	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6048941	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6048945	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6048946	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6048949	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6048950	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6048952	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048956	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61035931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6106685	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6114201	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6114206	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6114208	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6114209	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6515375	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67567111	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67997662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7265178	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73318135	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs734801	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8114619	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8115417	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8115423	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8116859	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8121147	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8121283	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8121405	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs911119	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv20263	chr20:23593820-23594562	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7270413	CST3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23583400-23594000	Weak transcription	Right Atrium	heart
2	chr20:23587000-23595600	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr20:23587800-23594000	Weak transcription	Colon Smooth Muscle	Colon
4	chr20:23588200-23594800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr20:23590000-23594000	Weak transcription	Brain Hippocampus Middle	brain
6	chr20:23590400-23595000	Weak transcription	Brain Anterior Caudate	brain
7	chr20:23592200-23595400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr20:23592400-23594800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr20:23592600-23595400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr20:23593000-23595200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr20:23593200-23594000	Weak transcription	Brain Germinal Matrix	brain
12	chr20:23593400-23595200	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr20:23593600-23594000	Enhancers	Stomach Smooth Muscle	stomach
14	chr20:23593600-23595200	Enhancers	Ovary	ovary

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