Variant report

Variant	rs6671589
Chromosome Location	chr1:85702868-85702869
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85689392..85691785-chr1:85702623..85704408,2	K562	blood:
2	chr1:85665334..85668152-chr1:85701558..85704505,3	MCF-7	breast:
3	chr1:85690285..85692339-chr1:85702623..85704270,2	K562	blood:

Variant related genes	Relation type
ENSG00000097096	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10493762	0.83[JPT][hapmap]
rs11161556	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11161574	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11161584	0.87[EUR][1000 genomes]
rs11577656	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11583836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12065422	0.86[MEX][hapmap]
rs12563295	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17122364	0.84[JPT][hapmap]
rs17123650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2054238	0.83[JPT][hapmap]
rs2252408	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2647396	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2735587	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2735591	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2735592	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2735593	0.81[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2735594	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36006436	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4255398	0.81[EUR][1000 genomes]
rs4907139	0.81[CHB][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.81[EUR][1000 genomes]
rs4949892	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949926	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60156243	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6693365	0.89[EUR][1000 genomes]
rs709790	0.80[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs72722613	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72722616	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72722624	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72722631	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72722638	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72722641	0.98[ASN][1000 genomes]
rs72722643	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7366220	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7531640	0.97[GIH][hapmap]

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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6671589	C1orf52	Cis_1M	lymphoblastoid	RTeQTL
rs6671589	C1orf52	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85687000-85709600	Weak transcription	Aorta	Aorta
2	chr1:85696400-85705600	Weak transcription	Fetal Heart	heart
3	chr1:85702000-85705800	Weak transcription	Pancreas	Pancrea

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