Variant report

Variant	rs10201530
Chromosome Location	chr2:77256291-77256292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10172719	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10183094	0.95[CEU][hapmap]
rs10183619	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs10183642	0.81[EUR][1000 genomes]
rs10186912	0.81[EUR][1000 genomes]
rs10187466	0.85[YRI][hapmap]
rs10190179	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10190198	0.95[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10190443	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10190510	0.80[CEU][hapmap]
rs10192262	0.86[TSI][hapmap];0.85[YRI][hapmap]
rs10193309	0.81[CEU][hapmap]
rs10196630	0.81[EUR][1000 genomes]
rs10196749	0.80[EUR][1000 genomes]
rs10196758	0.81[EUR][1000 genomes]
rs10196801	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs10196895	0.81[EUR][1000 genomes]
rs10196939	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs10198799	0.92[LWK][hapmap];1.00[YRI][hapmap]
rs10199256	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10520176	0.82[YRI][hapmap]
rs11126576	0.85[YRI][hapmap]
rs11896560	0.85[YRI][hapmap]
rs1252021	0.82[YRI][hapmap]
rs12621674	0.83[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs12987907	0.86[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs12992834	0.86[EUR][1000 genomes]
rs13013784	0.86[EUR][1000 genomes]
rs13385651	0.82[YRI][hapmap]
rs13385727	0.85[YRI][hapmap]
rs13422716	0.88[TSI][hapmap]
rs13427438	0.81[EUR][1000 genomes]
rs13427514	0.81[EUR][1000 genomes]
rs1345136	0.82[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1348824	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1348826	0.84[CEU][hapmap]
rs1348827	0.84[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1348831	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1374388	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1374389	0.86[EUR][1000 genomes]
rs1374390	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs1446692	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1446693	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1446695	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1446697	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1446698	0.95[CEU][hapmap];0.89[CHB][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1446701	0.96[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1446702	0.86[EUR][1000 genomes]
rs1446703	0.96[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1446704	0.96[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs1446705	0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1446707	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1446710	0.81[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs1446712	0.83[EUR][1000 genomes]
rs1446724	0.81[CEU][hapmap];1.00[TSI][hapmap]
rs1446725	0.81[CEU][hapmap];1.00[TSI][hapmap]
rs1470504	0.81[CEU][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs1470505	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs1470506	0.81[EUR][1000 genomes]
rs1470507	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1470508	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs1542186	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs1584234	0.84[CEU][hapmap]
rs1584235	0.81[EUR][1000 genomes]
rs1584236	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1584237	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs1596913	0.81[CEU][hapmap]
rs17013592	0.96[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs17013595	0.96[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs1997468	0.85[YRI][hapmap]
rs2028913	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2121409	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2121410	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2121411	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2197603	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2860937	0.81[EUR][1000 genomes]
rs2860938	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34372910	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34632326	0.85[EUR][1000 genomes]
rs35038238	0.86[EUR][1000 genomes]
rs35659577	0.86[EUR][1000 genomes]
rs4143794	0.83[EUR][1000 genomes]
rs4143796	0.81[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs4324338	0.83[CEU][hapmap]
rs4853283	0.85[YRI][hapmap]
rs4853286	0.85[EUR][1000 genomes]
rs4853287	0.86[EUR][1000 genomes]
rs4853288	0.86[EUR][1000 genomes]
rs4853289	0.86[EUR][1000 genomes]
rs4853291	0.87[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56314043	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6547104	0.82[YRI][hapmap]
rs6547110	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6547114	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6547115	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6547116	0.88[EUR][1000 genomes]
rs6547117	0.92[CEU][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs6547118	0.96[CEU][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs6708058	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6718391	0.85[EUR][1000 genomes]
rs6718440	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6719689	0.85[YRI][hapmap]
rs6732462	0.96[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6739222	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs6743454	0.85[EUR][1000 genomes]
rs715280	0.85[YRI][hapmap]
rs727000	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7422204	0.85[LWK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap]
rs7561361	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7563917	0.85[CEU][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7569624	0.89[EUR][1000 genomes]
rs7573982	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs7586363	0.85[YRI][hapmap]
rs7591186	0.86[EUR][1000 genomes]
rs7597923	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7604936	0.86[EUR][1000 genomes]
rs7605187	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs765572	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9309508	0.85[YRI][hapmap]
rs9309509	0.85[YRI][hapmap]
rs992313	0.88[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834266	chr2:77120236-77287504	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv949670	chr2:77125218-77712607	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv519950	chr2:77213103-77256291	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv997284	chr2:77233426-77303198	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10201530	LRRTM4	cis	cerebellum	SCAN
rs10201530	MRPL19	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:77255000-77256600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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