Variant report

Variant	rs6776120
Chromosome Location	chr3:160630267-160630268
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160472665..160476434-chr3:160627651..160631285,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260572	Chromatin interaction
ENSG00000163590	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11709802	0.84[JPT][hapmap]
rs12485723	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12696110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1348977	0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs1374795	1.00[CEU][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs1447616	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1447617	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1447624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1839014	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1839018	0.87[GIH][hapmap]
rs1868104	0.85[JPT][hapmap]
rs1868106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2028988	0.85[JPT][hapmap]
rs4679667	0.93[JPT][hapmap]
rs6441333	0.86[ASN][1000 genomes]
rs6441334	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6441335	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6441336	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6770488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6785844	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs6789195	0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6796612	0.90[EUR][1000 genomes]
rs6797498	0.85[JPT][hapmap]
rs6799391	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6800092	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6801330	0.82[GIH][hapmap]
rs7610732	0.85[JPT][hapmap]
rs7629374	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7636886	0.86[ASN][1000 genomes]
rs9814174	0.86[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv519474	chr3:160620205-160630267	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6776120	C3orf57	cis	parietal	SCAN
rs6776120	C3orf57	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160630200-160641400	Weak transcription	Psoas Muscle	Psoas

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