Variant report

Variant	rs669960
Chromosome Location	chr8:61550764-61550765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr8:61550749-61551078	K562	blood:	n/a	chr8:61550893-61550906 chr8:61550894-61550905 chr8:61550893-61550904 chr8:61550893-61550906
2	CEBPB	chr8:61550705-61551017	A549	lung:	n/a	chr8:61550893-61550906 chr8:61550894-61550905 chr8:61550893-61550904 chr8:61550893-61550906

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:61549221..61552065-chr8:61563903..61565606,2	MCF-7	breast:
2	chr8:61549271..61552282-chr8:61563024..61565421,3	K562	blood:

Variant related genes	Relation type
ENSG00000228862	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10100740	0.89[CEU][hapmap]
rs10109278	0.89[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs10957141	0.89[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs10957146	0.89[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs10957149	0.89[CEU][hapmap]
rs11778529	0.89[CEU][hapmap]
rs11778772	0.89[CEU][hapmap]
rs11778888	0.89[CEU][hapmap]
rs11782178	0.89[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs11786146	0.89[CEU][hapmap]
rs11988528	0.94[CEU][hapmap]
rs12678694	0.89[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs2625443	0.85[ASN][1000 genomes]
rs2680299	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2875966	0.89[CEU][hapmap]
rs585995	0.89[ASN][1000 genomes]
rs586110	0.84[ASN][1000 genomes]
rs602724	0.89[CEU][hapmap]
rs603239	0.89[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs610455	0.85[MEX][hapmap]
rs621279	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6471883	0.89[CEU][hapmap]
rs6471884	0.89[CEU][hapmap]
rs6471893	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs649634	0.89[CEU][hapmap];0.92[MEX][hapmap]
rs657087	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs664796	0.89[CEU][hapmap]
rs671275	0.95[CEU][hapmap];0.89[TSI][hapmap]
rs684573	0.89[CEU][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap]
rs6987523	0.89[CEU][hapmap]
rs6993237	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs6996344	0.89[CEU][hapmap];0.83[TSI][hapmap]
rs7357376	0.89[CEU][hapmap]
rs7820349	0.89[CEU][hapmap]
rs7822391	0.89[CEU][hapmap]
rs9437	0.89[CEU][hapmap];0.93[MEX][hapmap];0.86[TSI][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	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv530383	chr8:61431756-61605551	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv831335	chr8:61497540-61688992	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS 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 target site	33 gene(s)	inside rSNPs	diseases
4	nsv890945	chr8:61522008-61707725	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs669960	LOC643763	cis	parietal	SCAN
rs669960	RAB2	cis	uninvolved skin	skin_eQTL
rs669960	RAB2A	Cis_1M	lymphoblastoid	RTeQTL
rs669960	RAB2	cis	multi-tissue	Pritchard
rs669960	RAB2	cis	lesional skin	skin_eQTL
rs669960	RAB2	cis	normal skin	skin_eQTL

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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