Variant report

Variant	rs7509675
Chromosome Location	chr21:46054626-46054627
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1076849	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs10854463	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs11910263	0.84[LWK][hapmap]
rs11910292	0.82[LWK][hapmap]
rs12106369	0.86[JPT][hapmap]
rs12482870	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs12626853	0.82[JPT][hapmap]
rs12627686	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13048478	0.89[JPT][hapmap]
rs13051885	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1883039	0.83[CEU][hapmap];0.83[CHD][hapmap];0.84[MEX][hapmap]
rs1883041	0.83[CEU][hapmap]
rs2020088	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2073437	0.86[JPT][hapmap]
rs2225433	0.81[JPT][hapmap]
rs2256361	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs2256490	0.82[CEU][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs2256496	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs2329835	0.82[ASW][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs2329845	0.82[JPT][hapmap]
rs2838595	0.85[ASN][1000 genomes]
rs2838601	0.90[ASN][1000 genomes]
rs2838602	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs2838610	0.87[CEU][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs2838611	0.87[CEU][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2838612	0.86[JPT][hapmap]
rs2838614	0.87[CEU][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs2838617	0.82[CEU][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs2838618	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs2838619	0.81[JPT][hapmap]
rs2838622	0.82[JPT][hapmap]
rs2838624	0.82[CEU][hapmap]
rs2838625	0.82[CEU][hapmap];0.83[CHD][hapmap];0.84[MEX][hapmap]
rs2838627	0.83[CEU][hapmap];0.80[JPT][hapmap]
rs28542851	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2876970	0.95[CEU][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28817630	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4050979	0.81[JPT][hapmap]
rs450639	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs463217	0.86[CEU][hapmap]
rs4818728	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs4818946	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4818947	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4818950	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818951	0.87[ASN][1000 genomes]
rs4818953	0.87[CEU][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs62219767	0.83[ASN][1000 genomes]
rs6518197	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7275203	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs7275666	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs7276421	0.87[CEU][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs7276859	0.82[JPT][hapmap]
rs7280471	0.87[CEU][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs743495	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs762431	0.87[CEU][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap]
rs762436	0.82[LWK][hapmap]
rs8126553	0.85[ASN][1000 genomes]
rs8126811	0.82[JPT][hapmap]
rs8127342	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8129802	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8131142	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8132337	0.90[ASN][1000 genomes]
rs9284507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9306112	0.86[JPT][hapmap]
rs9808722	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9979457	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9980129	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9982138	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9983892	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs9984726	0.86[CEU][hapmap];0.85[JPT][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7509675	C21orf88	cis	parietal	SCAN
rs7509675	SIK1	cis	cerebellum	SCAN
rs7509675	KRTAP10-5	cis	parietal	SCAN
rs7509675	KRTAP12-2	cis	cerebellum	SCAN
rs7509675	TMPRSS2	cis	cerebellum	SCAN
rs7509675	C21orf70	cis	parietal	SCAN
rs7509675	UMODL1	cis	cerebellum	SCAN
rs7509675	U2AF1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46049000-46056800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr21:46049200-46060400	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links