Variant report

Variant	rs6016
Chromosome Location	chr1:169512120-169512121
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169449555..169458933-chr1:169508181..169519645,22	MCF-7	breast:
2	chr1:169453402..169457978-chr1:169510259..169517954,11	MCF-7	breast:
3	chr1:169510436..169512418-chr1:169514269..169516717,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213062	Chromatin interaction
ENSG00000117479	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10800450	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10800453	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10919178	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1121789	0.95[CEU][hapmap];0.82[CHB][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11579441	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12127364	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1557570	0.80[CEU][hapmap];0.81[YRI][hapmap]
rs2009814	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2187952	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2187953	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2213866	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2213867	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2227244	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239851	0.94[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420373	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3766109	0.95[CEU][hapmap];0.85[CHB][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766110	0.81[GIH][hapmap]
rs3820060	0.81[GIH][hapmap]
rs4524	0.94[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4525	0.94[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656187	0.95[CEU][hapmap];0.85[CHB][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656684	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4656685	0.95[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6017	0.94[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.96[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6021	0.95[CEU][hapmap];0.85[CHB][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6030	0.92[CHB][hapmap];0.84[GIH][hapmap]
rs6032	0.95[CEU][hapmap];0.85[CHB][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662593	0.81[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670393	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6675244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535409	0.80[ASN][1000 genomes]
rs9287090	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9287092	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9332595	0.81[GIH][hapmap]
rs9332599	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9332600	0.94[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332619	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9332620	0.81[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9332627	0.95[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332635	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9332643	0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9332651	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9332655	0.90[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9332667	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs970741	0.95[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs974793	0.95[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6016	DCAF6	cis	parietal	SCAN
rs6016	CREG1	cis	parietal	SCAN
rs6016	C1orf112	cis	parietal	SCAN
rs6016	RXRG	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169496000-169515200	Strong transcription	Liver	Liver
2	chr1:169498400-169524000	Weak transcription	Placenta	Placenta
3	chr1:169499000-169519000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:169500200-169526800	Weak transcription	Left Ventricle	heart
5	chr1:169504000-169515000	Strong transcription	HepG2	liver
6	chr1:169505800-169534800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:169506200-169542800	Weak transcription	Right Ventricle	heart
8	chr1:169507000-169530800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:169508800-169513200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:169509600-169515600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:169510200-169515800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:169510600-169513600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:169510800-169513400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:169510800-169515600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr1:169511000-169520000	Strong transcription	Primary neutrophils fromperipheralblood	blood

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