Variant report

Variant	rs7275666
Chromosome Location	chr21:46084675-46084676
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:46083230..46085018-chr21:46086422..46088371,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221864	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10854463	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1123949	0.81[GIH][hapmap]
rs12106369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12482870	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13046903	0.80[ASN][1000 genomes]
rs13051885	0.86[JPT][hapmap]
rs1883039	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1883041	0.90[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2073437	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2210284	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2225433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2256361	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2256490	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2256496	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2329838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2329839	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2329840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2329841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2329842	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2329843	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2329893	0.81[GIH][hapmap]
rs2838602	0.82[JPT][hapmap]
rs2838610	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs2838611	1.00[JPT][hapmap]
rs2838612	0.82[JPT][hapmap]
rs2838614	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2838617	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2838618	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2838619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838623	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2838624	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2838625	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2838627	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2838634	0.90[CHB][hapmap]
rs28542851	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs34979768	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35163632	0.80[ASN][1000 genomes]
rs3966427	0.84[ASN][1000 genomes]
rs4050979	0.86[JPT][hapmap]
rs4818728	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4818947	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs4818950	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs4818953	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs5013900	0.81[GIH][hapmap]
rs7275203	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7276421	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7277758	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7280471	1.00[JPT][hapmap]
rs7282198	0.84[EUR][1000 genomes]
rs7282421	0.95[ASN][1000 genomes]
rs7509675	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs762431	0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs8127265	0.81[GIH][hapmap]
rs8129802	0.91[JPT][hapmap]
rs8132352	0.81[JPT][hapmap]
rs8134266	0.81[GIH][hapmap]
rs926193	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9284507	0.91[JPT][hapmap]
rs9306111	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9306112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9974195	0.93[ASN][1000 genomes]
rs9983049	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9983892	0.96[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9984726	0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065798	chr21:45941000-46097463	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv869108	chr21:45941000-46097463	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv544476	chr21:45941000-46097463	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv913950	chr21:45985068-46097463	Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7275666	KRTAP12-2	cis	cerebellum	SCAN
rs7275666	RRP1B	cis	parietal	SCAN
rs7275666	TFF1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46079200-46086600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr21:46079400-46089600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr21:46084600-46084800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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