Variant report

Variant	rs55959738
Chromosome Location	chr6:133215578-133215579
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:133215147..133217831-chr6:133244049..133245701,2	MCF-7	breast:
2	chr6:133215054..133218379-chr6:133238674..133241555,3	MCF-7	breast:
3	chr6:133150152..133152401-chr6:133214566..133217408,2	MCF-7	breast:
4	chr6:133139979..133142138-chr6:133214137..133215920,2	MCF-7	breast:
5	chr6:133214987..133216663-chr6:133252701..133254390,2	MCF-7	breast:
6	chr6:133134365..133138473-chr6:133214191..133217735,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206754	Chromatin interaction
ENSG00000221500	Chromatin interaction
ENSG00000112306	Chromatin interaction
ENSG00000200534	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10457593	0.85[ASN][1000 genomes]
rs10457595	0.85[ASN][1000 genomes]
rs10484628	0.85[ASN][1000 genomes]
rs11154698	0.85[ASN][1000 genomes]
rs11758796	0.96[ASN][1000 genomes]
rs12190684	0.85[ASN][1000 genomes]
rs12191058	0.85[ASN][1000 genomes]
rs12193474	0.88[ASN][1000 genomes]
rs12194802	0.85[ASN][1000 genomes]
rs12195249	0.85[ASN][1000 genomes]
rs12196336	0.85[ASN][1000 genomes]
rs12198970	0.92[ASN][1000 genomes]
rs12200848	0.85[ASN][1000 genomes]
rs12201540	0.85[ASN][1000 genomes]
rs12202407	0.85[ASN][1000 genomes]
rs12203738	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12204693	0.85[ASN][1000 genomes]
rs12204740	0.85[ASN][1000 genomes]
rs12204863	0.85[ASN][1000 genomes]
rs12207011	0.85[ASN][1000 genomes]
rs12211425	0.85[ASN][1000 genomes]
rs12212934	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12215084	0.85[ASN][1000 genomes]
rs12215088	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12215486	0.85[ASN][1000 genomes]
rs17061751	0.85[ASN][1000 genomes]
rs28693848	0.85[ASN][1000 genomes]
rs28706652	0.81[ASN][1000 genomes]
rs34334052	0.92[ASN][1000 genomes]
rs3778173	0.85[ASN][1000 genomes]
rs3778175	0.85[ASN][1000 genomes]
rs55708537	0.85[ASN][1000 genomes]
rs56170227	0.85[ASN][1000 genomes]
rs59585087	0.97[AFR][1000 genomes]
rs59740783	0.92[ASN][1000 genomes]
rs60062075	0.85[ASN][1000 genomes]
rs60412119	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425110	0.85[ASN][1000 genomes]
rs62425113	0.85[ASN][1000 genomes]
rs62425114	0.85[ASN][1000 genomes]
rs62425132	0.85[ASN][1000 genomes]
rs62425133	0.85[ASN][1000 genomes]
rs62425137	0.85[ASN][1000 genomes]
rs62426668	0.96[ASN][1000 genomes]
rs62426674	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv869855	chr6:133190265-133244259	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55959738	C6orf192	Cis_1M	lymphoblastoid	RTeQTL
rs55959738	C6orf192	cis	multi-tissue	Pritchard

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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