Variant report

Variant	rs4815224
Chromosome Location	chr20:23594112-23594113
allele	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: 112 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1010117	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1011226	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1064039	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1158167	0.90[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12624424	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12625182	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12625716	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12710327	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13037490	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13038305	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13038337	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13038990	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13039536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13040663	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13041070	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13043266	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]
rs13043610	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1555355	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17751897	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016161	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2067488	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2208289	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2254635	0.89[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs2405367	0.90[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap]
rs2405392	0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2405393	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2424582	0.90[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[ASN][1000 genomes]
rs28703706	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3004139	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3004145	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3088162	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34374560	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34746357	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34792920	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34897231	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34911568	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35488434	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35573837	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35610040	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35782710	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35966482	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3761280	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3761281	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3787498	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3787499	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3810575	0.90[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3827141	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3827142	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3827143	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4346460	0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4815222	0.90[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4815223	0.89[CEU][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5030707	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55897275	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56077567	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56371840	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56388902	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57549987	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59059917	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036461	0.90[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6036463	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6036465	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6036469	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6036470	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036471	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036474	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6036476	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036478	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048920	0.90[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048922	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048923	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048924	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048925	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048926	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048928	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6048929	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6048930	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6048933	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048936	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6048937	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6048939	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6048941	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6048945	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6048946	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6048949	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6048950	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6048952	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048956	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61035931	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6106685	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6114201	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6114206	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6114208	0.90[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6114209	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6515375	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67567111	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67997662	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71334202	0.82[EUR][1000 genomes]
rs7265178	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7270413	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73318135	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs734801	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8114619	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8115417	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8115423	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8116859	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8121147	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8121283	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8121405	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs911119	0.89[CEU][hapmap];1.00[JPT][hapmap];0.84[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4815224	CST3	cis	multi-tissue	Pritchard
rs4815224	CST3	cis	cerebellum	SCAN
rs4815224	CST3	Cis_1M	lymphoblastoid	RTeQTL
rs4815224	CST3	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23587000-23595600	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr20:23588200-23594800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr20:23590400-23595000	Weak transcription	Brain Anterior Caudate	brain
4	chr20:23592200-23595400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr20:23592400-23594800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr20:23592600-23595400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr20:23593000-23595200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr20:23593400-23595200	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr20:23593600-23595200	Enhancers	Ovary	ovary
10	chr20:23594000-23594200	Enhancers	Brain Hippocampus Middle	brain
11	chr20:23594000-23594400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr20:23594000-23594800	Enhancers	Adipose Nuclei	Adipose
13	chr20:23594000-23595000	Enhancers	Brain Germinal Matrix	brain
14	chr20:23594000-23595200	Enhancers	Right Atrium	heart
15	chr20:23594000-23595400	Enhancers	Rectal Smooth Muscle	rectum
16	chr20:23594000-23595800	Enhancers	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links