Variant report

Variant	rs538062
Chromosome Location	chr13:91793222-91793223
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:91785963..91788672-chr13:91792933..91795639,3	K562	blood:
2	chr13:91789885..91794115-chr13:91998675..92001805,5	K562	blood:
3	chr13:91785963..91788672-chr13:91792933..91794568,2	K562	blood:

Variant related genes	Relation type
ENSG00000215417	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1020800	0.85[EUR][1000 genomes]
rs1020801	0.85[EUR][1000 genomes]
rs1174782	0.88[EUR][1000 genomes]
rs1174784	0.85[EUR][1000 genomes]
rs1332218	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs148771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167003	0.96[EUR][1000 genomes]
rs16952571	0.96[EUR][1000 genomes]
rs287490	0.91[EUR][1000 genomes]
rs287491	0.89[EUR][1000 genomes]
rs287492	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs287493	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs287494	0.93[EUR][1000 genomes]
rs287495	0.92[EUR][1000 genomes]
rs287496	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287497	0.90[EUR][1000 genomes]
rs287498	0.90[EUR][1000 genomes]
rs287499	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287500	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287501	0.93[EUR][1000 genomes]
rs287502	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs287504	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287505	0.93[EUR][1000 genomes]
rs287506	0.94[EUR][1000 genomes]
rs287508	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287509	0.94[EUR][1000 genomes]
rs287510	0.94[EUR][1000 genomes]
rs287511	0.94[EUR][1000 genomes]
rs287512	0.94[EUR][1000 genomes]
rs287513	0.94[EUR][1000 genomes]
rs287514	0.96[EUR][1000 genomes]
rs287515	0.94[EUR][1000 genomes]
rs287516	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287517	0.96[EUR][1000 genomes]
rs287518	0.96[EUR][1000 genomes]
rs287522	0.96[EUR][1000 genomes]
rs287523	0.96[EUR][1000 genomes]
rs287524	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs287525	0.92[EUR][1000 genomes]
rs287526	0.96[EUR][1000 genomes]
rs287527	0.98[EUR][1000 genomes]
rs287528	0.96[EUR][1000 genomes]
rs287529	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs287533	0.91[GIH][hapmap];0.88[TSI][hapmap]
rs287535	0.82[EUR][1000 genomes]
rs3764129	0.88[EUR][1000 genomes]
rs476066	0.82[EUR][1000 genomes]
rs481037	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs492117	0.85[EUR][1000 genomes]
rs504180	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs505160	0.85[EUR][1000 genomes]
rs506173	0.85[EUR][1000 genomes]
rs506238	0.85[EUR][1000 genomes]
rs512524	0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs515029	0.85[EUR][1000 genomes]
rs515097	0.85[EUR][1000 genomes]
rs515850	0.85[EUR][1000 genomes]
rs521178	0.83[EUR][1000 genomes]
rs536365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs539504	0.85[EUR][1000 genomes]
rs543567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544464	0.85[EUR][1000 genomes]
rs549865	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550731	0.83[EUR][1000 genomes]
rs558827	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs568455	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs568694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571202	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs582256	0.96[EUR][1000 genomes]
rs583053	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs612195	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs613553	0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs620620	0.88[EUR][1000 genomes]
rs622426	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623637	0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs644953	0.85[EUR][1000 genomes]
rs647785	0.85[EUR][1000 genomes]
rs650892	0.84[EUR][1000 genomes]
rs657464	0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs665530	0.84[EUR][1000 genomes]
rs684050	0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs693016	0.83[EUR][1000 genomes]
rs693721	0.85[EUR][1000 genomes]
rs7324853	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs76384	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];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs922083	0.85[EUR][1000 genomes]
rs9515887	0.96[EUR][1000 genomes]
rs9523263	0.85[EUR][1000 genomes]
rs9560762	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932206	chr13:91370888-91878374	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1042947	chr13:91571040-92416897	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
3	nsv541871	chr13:91571040-92416897	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
4	nsv900880	chr13:91625722-91848290	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1803618	chr13:91669587-92277699	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1945 gene(s)	inside rSNPs	diseases
6	nsv900881	chr13:91704312-91829940	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1050259	chr13:91759549-92152078	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
8	nsv541872	chr13:91759549-92152078	Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
9	nsv832678	chr13:91771619-91932241	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs538062	GPC6	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:91782800-91793800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:91787600-91795800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr13:91789400-91793400	Weak transcription	Aorta	Aorta
4	chr13:91789400-91795000	Weak transcription	Fetal Kidney	kidney
5	chr13:91791000-91794600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr13:91791000-91794800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr13:91791600-91795400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:91792000-91793400	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr13:91792200-91796600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr13:91792600-91795000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr13:91792800-91793400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr13:91793200-91793400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr13:91793200-91794400	Enhancers	Fetal Muscle Leg	muscle

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