Variant report

Variant	rs6048929
Chromosome Location	chr20:23588855-23588856
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	MAX	chr20:23588842-23589453	HepG2	liver:	n/a	n/a

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

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

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1010117	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1011226	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1064039	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1158167	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12624424	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12625182	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12625716	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12710327	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13037490	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13038305	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13038337	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13038990	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13039536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13040663	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13041070	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13043266	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13043610	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1555355	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17751897	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2016161	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2067488	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2208289	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2254635	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2405367	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs2405392	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2405393	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2424582	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs28703706	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3004139	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3004145	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3088162	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34374560	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34746357	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34792920	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34897231	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34911568	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35488434	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35573837	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35610040	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs35782710	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35966482	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3761280	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3761281	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3787498	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3787499	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3810575	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3827141	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs3827142	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3827143	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4346460	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4815222	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4815223	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4815224	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5030707	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55897275	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56077567	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56371840	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56388902	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57549987	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59059917	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6036461	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6036463	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6036465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6036469	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6036470	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6036471	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6036474	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6036476	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036478	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048920	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6048922	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048923	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048924	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048925	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048926	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048928	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048930	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6048933	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6048936	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6048937	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048939	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6048941	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6048945	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6048946	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6048949	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6048950	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6048952	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048956	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61035931	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6106685	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6114201	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6114206	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6114208	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6114209	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6515375	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67567111	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67997662	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7265178	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7270413	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8115417	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8115423	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8116859	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8121147	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8121283	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8121405	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs911119	0.90[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][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
rs6048929	CST3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23583400-23594000	Weak transcription	Right Atrium	heart
2	chr20:23586600-23590000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:23586800-23589000	Enhancers	HepG2	liver
4	chr20:23587000-23595600	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr20:23587200-23589200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:23587200-23590400	Enhancers	Brain Anterior Caudate	brain
7	chr20:23587800-23589000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr20:23587800-23589000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr20:23587800-23589800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr20:23587800-23589800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr20:23587800-23590400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr20:23587800-23594000	Weak transcription	Colon Smooth Muscle	Colon
13	chr20:23588200-23593400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr20:23588200-23594800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr20:23588400-23589200	Weak transcription	Brain Hippocampus Middle	brain
16	chr20:23588600-23590400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr20:23588600-23590400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr20:23588800-23590600	Enhancers	HUES6 Cell Line	embryonic stem cell

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