Variant report

Variant	rs4852879
Chromosome Location	chr2:72823177-72823178
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10183056	0.84[GIH][hapmap]
rs10206555	0.84[GIH][hapmap]
rs1032982	0.90[CEU][hapmap]
rs10460572	0.84[GIH][hapmap]
rs10865392	1.00[CHD][hapmap];0.84[GIH][hapmap]
rs11126370	0.84[GIH][hapmap]
rs11126376	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11676555	0.90[CEU][hapmap]
rs11677707	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11679683	0.90[CEU][hapmap]
rs11685114	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11686713	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11893504	0.91[EUR][1000 genomes]
rs11898717	0.82[YRI][hapmap]
rs12471136	0.84[GIH][hapmap]
rs12471312	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12617074	0.81[EUR][1000 genomes]
rs12992973	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12996319	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12998681	0.84[GIH][hapmap]
rs13006497	1.00[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs13008041	0.83[GIH][hapmap]
rs13008258	0.84[GIH][hapmap]
rs13011477	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1400581	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1446887	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1446888	0.83[GIH][hapmap]
rs1446890	0.84[GIH][hapmap]
rs1446891	0.84[GIH][hapmap]
rs1446893	0.84[GIH][hapmap]
rs1446895	0.84[GIH][hapmap]
rs1446896	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1508061	0.90[CEU][hapmap]
rs1517185	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1596930	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1596931	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1911690	0.90[CEU][hapmap]
rs1947118	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2138683	0.84[GIH][hapmap]
rs2203679	0.90[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap]
rs2901146	0.90[CEU][hapmap]
rs3115351	0.89[GIH][hapmap]
rs4364045	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4852294	0.90[EUR][1000 genomes]
rs4852873	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4852874	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4852875	0.84[GIH][hapmap]
rs4852878	0.83[GIH][hapmap]
rs4852883	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs4852886	1.00[CEU][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs4852888	1.00[CEU][hapmap]
rs4852889	0.90[CEU][hapmap]
rs4852890	0.90[CEU][hapmap]
rs4852891	0.90[CEU][hapmap]
rs585938	0.84[GIH][hapmap]
rs589547	0.90[CEU][hapmap]
rs590345	0.86[CEU][hapmap]
rs632670	0.84[GIH][hapmap]
rs645489	0.84[GIH][hapmap]
rs647242	0.90[CEU][hapmap]
rs653220	0.90[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs6546781	0.90[CEU][hapmap]
rs663218	0.89[GIH][hapmap]
rs6708156	0.81[EUR][1000 genomes]
rs6714595	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs671721	0.84[GIH][hapmap]
rs6724529	1.00[CEU][hapmap]
rs6750766	0.84[GIH][hapmap]
rs6758593	0.90[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs688433	0.84[GIH][hapmap]
rs7420667	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7577238	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7588400	0.90[CEU][hapmap]
rs7591303	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs7600273	0.90[EUR][1000 genomes]
rs7601020	0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv874264	chr2:72593243-72901170	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv582208	chr2:72690622-72835886	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv834257	chr2:72701083-72853548	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv874265	chr2:72789764-72982609	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4852879	STAMBP	cis	cerebellum	SCAN
rs4852879	MPHOSPH10	cis	cerebellum	SCAN
rs4852879	AUP1	cis	parietal	SCAN
rs4852879	TGFA	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72809200-72833800	Weak transcription	Left Ventricle	heart
2	chr2:72820400-72823400	Weak transcription	Psoas Muscle	Psoas
3	chr2:72821400-72823200	Weak transcription	Ovary	ovary
4	chr2:72822800-72823200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:72823000-72823200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:72823000-72823600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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