Variant report

Variant	rs1988500
Chromosome Location	chr13:92462942-92462943
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs12050058	0.90[CHB][hapmap]
rs12431259	0.85[CHB][hapmap]
rs1330472	0.90[CHB][hapmap];0.93[CHD][hapmap]
rs1332091	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1332092	0.81[CHB][hapmap]
rs1394888	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412313	0.90[CHB][hapmap]
rs1505565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168278	0.84[ASN][1000 genomes]
rs168279	0.85[ASN][1000 genomes]
rs173141	0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs17668748	0.85[CHB][hapmap]
rs1827755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182926	0.81[ASN][1000 genomes]
rs1831563	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1831564	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1831565	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1831566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1847713	0.81[CHB][hapmap]
rs1847714	0.85[ASN][1000 genomes]
rs1847715	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1847716	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1847717	0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1854971	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1854972	0.91[CEU][hapmap];0.84[TSI][hapmap];0.80[YRI][hapmap];0.89[EUR][1000 genomes]
rs1854973	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1854976	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1854978	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1854979	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1854980	0.81[CHB][hapmap]
rs189376	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1929922	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1929923	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1929924	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1929925	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs193208	0.94[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap]
rs1999231	0.81[CHB][hapmap]
rs2352028	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2352029	0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2352030	0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2352202	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2352203	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938868	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2938869	0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2938873	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2938874	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2989991	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2989992	0.85[ASN][1000 genomes]
rs2989993	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2989994	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2989995	0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2989996	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2989997	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2989998	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2990003	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2990004	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2990007	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap]
rs3012005	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs342672	0.85[ASN][1000 genomes]
rs342702	0.81[ASN][1000 genomes]
rs342706	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs345443	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs345444	0.83[LWK][hapmap];0.89[YRI][hapmap]
rs345445	0.93[YRI][hapmap]
rs345449	0.85[ASN][1000 genomes]
rs345450	0.83[ASN][1000 genomes]
rs3783054	0.81[CHB][hapmap]
rs3864180	0.85[CHB][hapmap]
rs386885	0.89[YRI][hapmap]
rs400118	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.85[ASN][1000 genomes]
rs439700	0.85[ASN][1000 genomes]
rs459137	0.85[ASN][1000 genomes]
rs464160	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4771843	0.81[CHB][hapmap]
rs4771844	0.81[CHB][hapmap]
rs522812	0.81[ASN][1000 genomes]
rs528366	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.98[MKK][hapmap];0.82[YRI][hapmap]
rs535973	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs539065	0.85[ASN][1000 genomes]
rs543718	0.89[YRI][hapmap]
rs556483	0.85[ASN][1000 genomes]
rs556722	0.85[ASN][1000 genomes]
rs560244	0.85[ASN][1000 genomes]
rs570196	0.85[ASN][1000 genomes]
rs7320766	0.85[CHB][hapmap]
rs7336461	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7981572	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7985030	0.90[CHB][hapmap]
rs7986027	0.90[CHB][hapmap]
rs7987852	0.83[CHB][hapmap]
rs7990703	0.87[CEU][hapmap]
rs7995130	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs7995788	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs7997428	0.90[CHB][hapmap]
rs9301750	0.83[CHB][hapmap]
rs9301754	0.81[CHB][hapmap]
rs9301755	0.86[EUR][1000 genomes]
rs9301756	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs9515967	0.81[CHB][hapmap]
rs9515971	0.81[CHB][hapmap]
rs9515973	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9515975	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9515980	0.81[CHB][hapmap]
rs9515981	0.81[CHB][hapmap]
rs9523404	0.84[CHB][hapmap]
rs9523407	0.81[CHB][hapmap]
rs9523410	0.81[CHB][hapmap]
rs9523424	0.81[CHB][hapmap]
rs9556125	0.89[CHB][hapmap]
rs9560852	0.94[CHB][hapmap]
rs9560853	0.94[CHB][hapmap]
rs9560860	0.90[CHB][hapmap]
rs9560863	0.89[EUR][1000 genomes]
rs9560868	0.89[CHB][hapmap]
rs9560869	0.84[CHB][hapmap]
rs9560874	0.83[CHB][hapmap]
rs9560875	0.85[CHB][hapmap]
rs9560880	0.85[CHB][hapmap]
rs9560883	0.85[CHB][hapmap]
rs9589358	0.95[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049382	chr13:92024240-92521180	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv541873	chr13:92024240-92521180	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv529268	chr13:92267310-92531263	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv456065	chr13:92383193-92507887	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv562719	chr13:92383193-92507887	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv948820	chr13:92408505-92519053	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv524271	chr13:92419769-92501664	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv562720	chr13:92419769-92501664	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1036226	chr13:92421721-92501284	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1053048	chr13:92421721-92501558	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1053597	chr13:92421721-92502205	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv3378326	chr13:92445514-92816367	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv974112	chr13:92459668-92465750	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1988500	GPC5	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:92457400-92465600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:92458000-92463800	Weak transcription	Fetal Heart	heart
3	chr13:92458000-92464000	Weak transcription	Fetal Lung	lung
4	chr13:92459000-92463600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr13:92459200-92465000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:92459600-92463200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr13:92461000-92463400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr13:92461600-92464800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr13:92461800-92463800	Weak transcription	Colon Smooth Muscle	Colon
10	chr13:92462400-92463800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr13:92462400-92464400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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