Variant report

Variant	rs12669586
Chromosome Location	chr7:87666274-87666275
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:87665716..87668051-chr7:87668778..87671387,2	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10235694	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10241669	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10266440	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10279744	0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10279940	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10282572	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10435251	0.81[EUR][1000 genomes]
rs10952906	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11770982	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11972409	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12704375	0.88[EUR][1000 genomes]
rs12704380	0.96[CEU][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs12704381	0.94[EUR][1000 genomes]
rs1613737	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1623535	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1629569	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1631368	0.92[EUR][1000 genomes]
rs1637487	0.94[EUR][1000 genomes]
rs1637488	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1637489	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs1637492	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1637494	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs1637495	0.83[EUR][1000 genomes]
rs1637496	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1637497	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1637498	0.93[EUR][1000 genomes]
rs1637499	0.96[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs1637500	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1637502	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs1637503	0.92[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs1637504	0.88[EUR][1000 genomes]
rs1637505	0.86[EUR][1000 genomes]
rs1637506	0.87[EUR][1000 genomes]
rs1637508	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1688886	0.96[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1688887	0.93[EUR][1000 genomes]
rs1688888	0.96[CEU][hapmap];0.84[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs1688890	0.96[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1688891	0.96[CEU][hapmap];0.84[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs1688893	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1688894	0.94[EUR][1000 genomes]
rs1688895	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1688896	0.94[EUR][1000 genomes]
rs1688897	0.94[EUR][1000 genomes]
rs1688898	0.95[EUR][1000 genomes]
rs1688899	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1688901	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1688902	0.96[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs17150161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2021741	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs2022160	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2022163	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2022164	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2022555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2023533	0.96[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2024018	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2024019	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2079422	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2079423	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2097917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108087	0.96[CEU][hapmap]
rs2158766	0.96[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2282948	0.96[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2282949	0.96[CEU][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2282951	0.85[CEU][hapmap]
rs2299190	0.84[CEU][hapmap];0.82[MEX][hapmap]
rs2373486	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2373487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28432284	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28794871	0.87[EUR][1000 genomes]
rs4728718	0.91[EUR][1000 genomes]
rs56160917	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56897831	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59135798	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60069756	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6465124	0.86[EUR][1000 genomes]
rs6465126	0.82[EUR][1000 genomes]
rs6465127	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6958024	0.82[CHB][hapmap]
rs7777040	0.82[CHB][hapmap]
rs7786538	0.88[EUR][1000 genomes]
rs7799148	0.82[CHB][hapmap]
rs7802934	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7803521	0.94[EUR][1000 genomes]
rs7809391	0.82[EUR][1000 genomes]
rs9641021	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9641022	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1015862	chr7:87075394-88049798	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1023352	chr7:87418818-88192925	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv539005	chr7:87418818-88192925	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv525073	chr7:87535096-87812968	Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1018868	chr7:87639899-87671754	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1021303	chr7:87646755-87672380	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12669586	RNF125	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:87663000-87671200	Weak transcription	Dnd41	blood

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