Variant report

Variant	rs6801330
Chromosome Location	chr3:160595284-160595285
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11711152	0.81[JPT][hapmap]
rs11713093	0.84[JPT][hapmap]
rs11718966	0.81[JPT][hapmap]
rs11922296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12107243	0.89[CEU][hapmap]
rs12488621	0.85[CEU][hapmap]
rs12494133	1.00[CEU][hapmap]
rs13071999	0.81[JPT][hapmap]
rs13073059	0.81[JPT][hapmap]
rs13079241	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13325518	1.00[CEU][hapmap]
rs1348976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1374789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1374790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1374795	0.95[JPT][hapmap]
rs1447610	0.81[JPT][hapmap]
rs1447615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1447622	0.90[JPT][hapmap]
rs1839018	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1868107	0.81[JPT][hapmap]
rs1868109	0.90[JPT][hapmap]
rs2279106	0.89[CEU][hapmap]
rs4679917	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4679918	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4679920	0.85[JPT][hapmap]
rs6441338	0.81[JPT][hapmap]
rs6763838	0.85[CEU][hapmap]
rs6768115	0.81[JPT][hapmap]
rs6774725	0.81[JPT][hapmap]
rs6776120	0.82[GIH][hapmap]
rs6791327	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6799779	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7429731	0.85[CEU][hapmap]
rs7641892	0.81[JPT][hapmap]
rs7649954	0.85[CEU][hapmap]
rs898683	0.85[CEU][hapmap]
rs898684	0.85[CEU][hapmap]
rs898685	0.84[CEU][hapmap]
rs935497	0.81[JPT][hapmap]
rs956447	0.90[JPT][hapmap]
rs9844267	0.81[JPT][hapmap]
rs9857195	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9857482	0.80[JPT][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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv32963	chr3:160555238-160603116	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6801330	C3orf57	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160589000-160596000	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:160591800-160595600	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr3:160592200-160595600	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr3:160594000-160595400	Enhancers	Psoas Muscle	Psoas
5	chr3:160594600-160596200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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