Variant report

Variant	rs6048930
Chromosome Location	chr20:23592492-23592493
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23419497..23422715-chr20:23589979..23593117,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125823	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1011226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1158167	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs12625716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13037490	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13038305	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13039536	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13043266	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13043610	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17751897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
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]
rs2424582	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3088162	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35610040	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3787498	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3787499	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3810575	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3827141	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3827142	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3827143	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4346460	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs4815222	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs4815223	0.94[CEU][hapmap]
rs4815224	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6036461	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs6036465	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6036478	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6048920	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs6048923	0.91[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs6048928	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6048929	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6048952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6048956	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6114201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6114208	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs6515375	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs8116859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs911119	0.95[CEU][hapmap];1.00[JPT][hapmap]

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
rs6048930	CST3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 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	chr20:23588200-23593400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr20:23588200-23594800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr20:23590000-23594000	Weak transcription	Brain Hippocampus Middle	brain
7	chr20:23590400-23595000	Weak transcription	Brain Anterior Caudate	brain
8	chr20:23590600-23592600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr20:23591200-23593600	Weak transcription	Ovary	ovary
10	chr20:23592200-23595400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr20:23592400-23594800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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