Variant report

Variant	rs2836921
Chromosome Location	chr21:40516070-40516071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40500620..40503419-chr21:40514957..40517352,2	MCF-7	breast:
2	chr21:40187682..40190648-chr21:40515051..40517560,2	K562	blood:
3	chr21:40515045..40517446-chr21:40522211..40524876,3	MCF-7	breast:

Extended variants
information (count: 98 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1065242	0.91[EUR][1000 genomes]
rs11910151	0.91[EUR][1000 genomes]
rs11911112	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11911149	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12481860	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12482156	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12482181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12482857	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12483216	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12710453	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13047550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13048178	0.92[EUR][1000 genomes]
rs13049280	0.91[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13052882	0.93[EUR][1000 genomes]
rs13339986	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13625	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs14194	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1541102	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs1571709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1984022	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2026265	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2026267	0.84[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2150415	0.95[CEU][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap]
rs2234543	0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2735306	0.88[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2776307	0.88[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2776309	0.88[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2836915	0.82[MKK][hapmap]
rs2836920	0.84[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2836923	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836924	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836927	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836928	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836932	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2836933	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs2836938	0.90[EUR][1000 genomes]
rs2836939	1.00[YRI][hapmap]
rs2836944	0.83[EUR][1000 genomes]
rs2836955	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2836957	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs2836964	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs2836965	0.96[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs2836967	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs2836968	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs2836974	0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs34035316	0.84[EUR][1000 genomes]
rs34176878	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34294410	0.93[EUR][1000 genomes]
rs34394827	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34478864	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34592564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34978594	0.84[EUR][1000 genomes]
rs35064900	0.92[EUR][1000 genomes]
rs35386515	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35391055	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35571600	0.83[EUR][1000 genomes]
rs35774464	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36113648	0.93[EUR][1000 genomes]
rs3945	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4817996	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56049536	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56112725	0.86[EUR][1000 genomes]
rs56306759	0.81[EUR][1000 genomes]
rs6517513	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517514	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517519	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517521	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517523	0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs6517526	0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs6517527	0.84[EUR][1000 genomes]
rs6517538	0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs66465538	0.80[AMR][1000 genomes]
rs68090597	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71184665	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7280375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7283516	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs73221174	0.87[EUR][1000 genomes]
rs73221193	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8127087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8128026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8128102	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs8128191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8128734	0.91[EUR][1000 genomes]
rs8129355	0.84[EUR][1000 genomes]
rs8130556	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8130984	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs8131965	0.85[EUR][1000 genomes]
rs8132285	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs8132295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8132333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8132419	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8132568	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9941894	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061831	chr21:40376316-40583555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv544443	chr21:40376316-40583555	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv3395554	chr21:40512728-40517052	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2836921	PSMG1	cis	Esophagus Mucosa	GTEx
rs2836921	HMGN1	cis	multi-tissue	Pritchard
rs2836921	HMGN1	cis	brain	seeQTL
rs2836921	PSMG1	cis	lymphoblastoid	seeQTL
rs2836921	BRWD1	cis	multi-tissue	Pritchard
rs2836921	CLIC6	cis	parietal	SCAN
rs2836921	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs2836921	DSCR2	cis	normal skin	skin_eQTL
rs2836921	LOC643790	trans	multi-tissue	Pritchard
rs2836921	DSCR3	cis	cerebellum	SCAN
rs2836921	PIGP	cis	parietal	SCAN
rs2836921	BRWD1	cis	cerebellum	SCAN
rs2836921	PSMG1	cis	parietal	SCAN
rs2836921	BRWD1	cis	parietal	SCAN
rs2836921	DSCR2	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40514200-40517000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr21:40514200-40520200	Weak transcription	Psoas Muscle	Psoas
3	chr21:40515000-40516400	Enhancers	Fetal Muscle Leg	muscle
4	chr21:40515800-40516400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links