Variant report

Variant	rs6656408
Chromosome Location	chr1:221314220-221314221
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10218738	0.85[EUR][1000 genomes]
rs10218739	0.85[EUR][1000 genomes]
rs1073166	0.87[EUR][1000 genomes]
rs10746408	0.87[EUR][1000 genomes]
rs10779421	0.85[EUR][1000 genomes]
rs10863580	0.84[EUR][1000 genomes]
rs10863582	0.80[EUR][1000 genomes]
rs10863584	0.84[EUR][1000 genomes]
rs10863585	0.87[EUR][1000 genomes]
rs10863589	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11118645	0.83[EUR][1000 genomes]
rs11118650	0.85[EUR][1000 genomes]
rs11118657	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12139572	0.83[EUR][1000 genomes]
rs1372665	0.87[EUR][1000 genomes]
rs1417921	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1442465	0.85[EUR][1000 genomes]
rs1539139	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1867071	0.85[EUR][1000 genomes]
rs1965817	0.87[EUR][1000 genomes]
rs1992480	0.85[EUR][1000 genomes]
rs2378435	0.85[EUR][1000 genomes]
rs4359036	0.83[EUR][1000 genomes]
rs4518910	0.85[EUR][1000 genomes]
rs4532839	0.88[EUR][1000 genomes]
rs6541171	0.85[EUR][1000 genomes]
rs6541172	0.85[EUR][1000 genomes]
rs6541179	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6541180	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6656596	0.88[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs6657690	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6664595	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6669742	0.85[EUR][1000 genomes]
rs6677416	0.85[EUR][1000 genomes]
rs6677487	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6678719	0.86[AMR][1000 genomes]
rs6694121	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs6696268	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7513152	0.85[EUR][1000 genomes]
rs7527151	0.85[EUR][1000 genomes]
rs7527891	0.85[EUR][1000 genomes]
rs7545437	0.85[EUR][1000 genomes]
rs894361	0.85[EUR][1000 genomes]
rs9431421	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9431432	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9431436	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs989463	0.87[EUR][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	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv873199	chr1:221136672-221451217	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6656408	C1orf115	cis	lymphoblastoid	seeQTL
rs6656408	RRP15	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221313600-221314600	Weak transcription	Fetal Lung	lung
2	chr1:221314200-221315200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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