Variant report

Variant	rs342706
Chromosome Location	chr13:92417058-92417059
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:92414642..92418617-chr13:92420339..92423769,4	K562	blood:
2	chr13:92296687..92299526-chr13:92415724..92417645,2	K562	blood:
3	chr13:92329658..92332164-chr13:92415917..92418730,3	K562	blood:
4	chr13:92416606..92418610-chr13:92424268..92426806,2	K562	blood:

Extended variants
information (count: 126 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs12050058	0.94[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs12430247	0.83[ASN][1000 genomes]
rs12430256	0.83[ASN][1000 genomes]
rs12431259	0.90[CHB][hapmap]
rs12873046	0.84[EUR][1000 genomes]
rs1330472	0.84[CHB][hapmap]
rs1332090	0.87[CEU][hapmap]
rs1332091	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1394888	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs1412313	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs1505565	0.94[CHB][hapmap]
rs168217	0.88[CEU][hapmap];0.80[TSI][hapmap]
rs168277	0.83[EUR][1000 genomes]
rs168278	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs168279	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs173141	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17668312	0.88[ASN][1000 genomes]
rs17668748	0.90[CHB][hapmap];0.96[CHD][hapmap]
rs1827755	0.95[CHB][hapmap];0.80[JPT][hapmap]
rs182926	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1831564	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs1847714	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1847715	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1847716	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1847717	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1854976	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1854977	0.88[CEU][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs1854978	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1854979	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs189376	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1929922	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1929923	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1929924	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1929925	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs193208	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1988500	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs2352028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs2352029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs2352030	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2352202	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs2938868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2938869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2938873	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2938874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2989990	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs2989991	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2989992	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2989993	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2989994	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2989995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2989996	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2989997	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2989998	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2990003	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2990004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap]
rs2990007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs3012005	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs342672	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs342673	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs342696	0.88[YRI][hapmap]
rs342701	0.88[CEU][hapmap];0.89[YRI][hapmap]
rs342702	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342704	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs342707	0.88[CEU][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs342708	0.88[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs345443	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs345444	0.87[CEU][hapmap]
rs345445	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs345449	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs345450	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3864180	0.81[CHB][hapmap]
rs386885	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs400118	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs439700	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs457306	0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs459137	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs464160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs464167	0.88[CEU][hapmap]
rs522812	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs528366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs535973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs539065	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs543718	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs556483	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs556722	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs560244	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs570196	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57676883	0.83[ASN][1000 genomes]
rs58499122	0.86[ASN][1000 genomes]
rs58505971	0.82[ASN][1000 genomes]
rs58932811	0.86[ASN][1000 genomes]
rs59464246	0.83[ASN][1000 genomes]
rs60993910	0.83[ASN][1000 genomes]
rs72647267	0.83[ASN][1000 genomes]
rs7320766	0.90[CHB][hapmap];0.92[CHD][hapmap]
rs7336461	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7981451	0.80[ASN][1000 genomes]
rs7985030	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs7986027	0.95[CHB][hapmap];0.96[CHD][hapmap]
rs7987852	0.89[CHB][hapmap]
rs7991916	0.88[CEU][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs7997428	0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap]
rs9515975	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs9556115	0.85[ASN][1000 genomes]
rs9556116	0.85[ASN][1000 genomes]
rs9556119	0.83[ASN][1000 genomes]
rs9556120	0.83[ASN][1000 genomes]
rs9556125	0.94[CHB][hapmap]
rs9560852	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs9560853	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs9560856	0.85[ASN][1000 genomes]
rs9560860	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs9560868	0.94[CHB][hapmap]
rs9560869	0.89[CHB][hapmap]
rs9560874	0.88[CHB][hapmap]
rs9560875	0.90[CHB][hapmap];0.92[CHD][hapmap]
rs9560880	0.90[CHB][hapmap]
rs9560883	0.90[CHB][hapmap]
rs9589358	1.00[CHB][hapmap];0.96[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv2753383	chr13:92226599-92462699	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	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
5	nsv456065	chr13:92383193-92507887	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv562719	chr13:92383193-92507887	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv948820	chr13:92408505-92519053	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs342706	GPC5	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:92383000-92419400	Weak transcription	Hela-S3	cervix
2	chr13:92416000-92419200	Weak transcription	Fetal Intestine Large	intestine
3	chr13:92417000-92417800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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