Variant report

Variant	rs12482870
Chromosome Location	chr21:46081379-46081380
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	chr21:46080081..46082771-chr21:46085171..46086703,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10854463	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12106369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13048478	0.85[JPT][hapmap]
rs13051885	0.85[JPT][hapmap]
rs1883039	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1883041	0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2073437	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2210284	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2225433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2256361	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[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];0.94[ASN][1000 genomes]
rs2256490	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2256496	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2329838	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2329839	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2329840	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2329841	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2329842	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2329843	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838602	0.81[JPT][hapmap]
rs2838610	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs2838611	0.91[JPT][hapmap]
rs2838612	0.81[JPT][hapmap]
rs2838614	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2838617	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2838618	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2838619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838623	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2838624	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2838625	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2838627	1.00[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2838634	0.90[CHB][hapmap]
rs28542851	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs34979768	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3966427	0.82[ASN][1000 genomes]
rs4818728	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4818947	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs4818950	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs4818953	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs7275203	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7275666	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]
rs7276421	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs7277758	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7280471	0.91[JPT][hapmap]
rs7282198	0.85[EUR][1000 genomes]
rs7282421	0.93[ASN][1000 genomes]
rs7509675	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs762431	0.87[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap]
rs8129802	0.91[JPT][hapmap]
rs926193	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9284507	0.91[JPT][hapmap]
rs9306111	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9306112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9974195	0.91[ASN][1000 genomes]
rs9983049	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9983892	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9984726	0.87[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.82[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
rs12482870	RRP1B	cis	parietal	SCAN
rs12482870	KRTAP12-2	cis	cerebellum	SCAN
rs12482870	TFF1	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46078200-46081600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr21:46079200-46086600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr21:46079400-46089600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr21:46080000-46081400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr21:46080200-46081400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr21:46080400-46081400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr21:46081000-46081600	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr21:46081200-46081800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
9	chr21:46081200-46082400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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