Variant report

Variant	rs4818953
Chromosome Location	chr21:46075223-46075224
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KRTAP12-4-1	chr21:46072303-46075583	NONHSAT082873

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10854463	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12106369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12482870	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs13051885	0.86[JPT][hapmap]
rs1883039	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1883041	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2073437	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2210284	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2225433	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2256361	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2256490	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2256496	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2329837	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2329838	0.91[ASN][1000 genomes]
rs2329839	0.91[ASN][1000 genomes]
rs2329840	0.91[ASN][1000 genomes]
rs2329841	0.91[ASN][1000 genomes]
rs2329842	0.90[ASN][1000 genomes]
rs2329843	0.90[ASN][1000 genomes]
rs2838601	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2838602	0.90[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2838610	0.91[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2838611	0.90[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2838612	0.82[JPT][hapmap]
rs2838614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838617	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838618	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838619	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2838623	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838624	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2838625	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2838627	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2838634	0.90[CHB][hapmap]
rs28542851	0.87[CEU][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs2876970	0.83[CEU][hapmap]
rs34979768	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3944594	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3966427	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4050979	0.86[JPT][hapmap]
rs463217	0.90[CEU][hapmap]
rs4818727	0.83[EUR][1000 genomes]
rs4818728	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4818947	0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4818950	0.90[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs4818952	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs68065001	0.81[AFR][1000 genomes]
rs7275203	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7275666	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7276421	0.90[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7277758	0.94[ASN][1000 genomes]
rs7280471	0.90[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7282421	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7509675	0.87[CEU][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs762431	0.87[ASW][hapmap];0.91[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs762433	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8129802	0.83[CEU][hapmap];0.91[JPT][hapmap]
rs8132352	0.81[JPT][hapmap]
rs926193	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9284507	0.86[CEU][hapmap];0.91[JPT][hapmap]
rs9306111	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9306112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9974195	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9983049	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9983892	0.87[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9984726	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[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
rs4818953	C21orf70	cis	parietal	SCAN
rs4818953	UMODL1	cis	cerebellum	SCAN
rs4818953	KRTAP12-2	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46073200-46075400	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr21:46073200-46075800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr21:46073200-46075800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr21:46073200-46076400	Enhancers	Primary T cells fromperipheralblood	blood
5	chr21:46073200-46076800	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr21:46073200-46076800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr21:46073400-46075400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr21:46073400-46076200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr21:46073400-46076600	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr21:46073600-46079800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr21:46073600-46080200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr21:46075000-46076000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links