Variant report

Variant	rs10882544
Chromosome Location	chr10:96885334-96885335
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10786187	0.90[EUR][1000 genomes]
rs10786189	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10786190	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10882538	0.81[EUR][1000 genomes]
rs10882540	0.81[EUR][1000 genomes]
rs10882543	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10882546	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11188189	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11188190	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11188192	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11188196	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11188197	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11188200	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12261370	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12764831	0.95[CEU][hapmap]
rs12769577	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12782731	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1575930	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16872	0.82[CHD][hapmap]
rs1854029	0.81[EUR][1000 genomes]
rs1854030	0.81[EUR][1000 genomes]
rs2449809	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2449810	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2478477	0.89[GIH][hapmap]
rs2478478	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs2478479	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2901829	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4119640	0.81[EUR][1000 genomes]
rs4532969	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs489807	0.91[CEU][hapmap]
rs509736	0.92[CEU][hapmap]
rs513661	0.89[CEU][hapmap]
rs585381	0.92[EUR][1000 genomes]
rs589801	0.92[CEU][hapmap]
rs591157	0.92[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs591171	0.92[CEU][hapmap]
rs592055	0.92[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs593207	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs594402	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs594448	0.92[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs604022	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs604373	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs610046	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs610579	0.80[EUR][1000 genomes]
rs611343	0.92[CEU][hapmap]
rs611416	0.90[EUR][1000 genomes]
rs612490	0.92[CEU][hapmap]
rs613340	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs614682	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs616721	0.81[EUR][1000 genomes]
rs620196	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs626415	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs627173	0.92[CEU][hapmap]
rs628102	0.92[CEU][hapmap]
rs632113	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs633345	0.92[CEU][hapmap]
rs634269	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs637465	0.92[CEU][hapmap]
rs637724	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs637939	0.92[CEU][hapmap]
rs638895	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs641198	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs644437	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs646845	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs648638	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs648695	0.92[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs6583979	0.80[EUR][1000 genomes]
rs6583980	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs659949	0.92[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs663473	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs664093	0.92[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs666679	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs666786	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs669360	0.92[CEU][hapmap]
rs672428	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs672860	0.92[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs675332	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs678165	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs679025	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs680918	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs682477	0.93[EUR][1000 genomes]
rs685607	0.96[CEU][hapmap]
rs688706	0.92[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs689207	0.92[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs7072133	0.81[EUR][1000 genomes]
rs7079861	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7082502	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7087492	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7087618	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7089303	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7094658	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs752415	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs752416	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7907627	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7907827	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7921561	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs815265	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs815266	0.92[EUR][1000 genomes]
rs815268	0.91[EUR][1000 genomes]
rs815269	0.92[EUR][1000 genomes]
rs815270	0.91[EUR][1000 genomes]
rs943313	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs943315	0.91[EUR][1000 genomes]

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	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv21432	chr10:96856006-96996043	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1046150	chr10:96865081-96885334	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases
5	nsv551985	chr10:96870565-96920198	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10882544	PDLIM1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96882400-96889400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr10:96883200-96886000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr10:96883400-96888400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr10:96883400-96889200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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