Variant report

Variant	rs16853578
Chromosome Location	chr3:143138333-143138334
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143127774..143129299-chr3:143137124..143139731,2	MCF-7	breast:
2	chr3:143137679..143139252-chr3:143142655..143144668,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PAQR9-5	chr3:143138239-143140079	ucscGeneNc_uc003euj_1

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10513200	0.84[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs10513201	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs10935491	0.94[ASN][1000 genomes]
rs10935492	0.95[ASN][1000 genomes]
rs11707045	0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs11707857	0.84[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs11719681	0.92[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs16846341	0.90[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16853522	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17757146	0.92[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs17757182	0.95[ASN][1000 genomes]
rs1875459	0.92[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs2360255	0.84[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs35233571	0.94[ASN][1000 genomes]
rs35358995	0.86[ASN][1000 genomes]
rs36125349	0.95[ASN][1000 genomes]
rs3860228	0.90[CEU][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs4311209	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4521222	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4839634	0.83[JPT][hapmap]
rs56078024	0.85[EUR][1000 genomes]
rs56080141	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56152928	0.94[ASN][1000 genomes]
rs61301417	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6770293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6782465	0.90[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6803041	0.80[JPT][hapmap]
rs73144735	0.83[EUR][1000 genomes]
rs73144736	0.83[EUR][1000 genomes]
rs73144740	0.85[ASN][1000 genomes]
rs73144743	0.91[ASN][1000 genomes]
rs73144745	0.90[ASN][1000 genomes]
rs73144749	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73144760	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73144769	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73144770	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73144771	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73144772	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73144773	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73144774	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73144777	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7374585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7617737	0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7627844	0.95[ASN][1000 genomes]
rs7652087	0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7652557	0.95[ASN][1000 genomes]
rs924576	0.90[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv2757894	chr3:142992697-143285979	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759184	chr3:142992697-143285979	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1011088	chr3:143135891-143163169	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16853578	UGT2B17	trans	lymphoblastoid	seeQTL
rs16853578	PLSCR4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143100600-143142600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:143129400-143140600	Weak transcription	NHDF-Ad	bronchial
3	chr3:143133200-143142800	Weak transcription	Primary B cells from cord blood	blood
4	chr3:143136600-143138600	Weak transcription	Aorta	Aorta
5	chr3:143137200-143138600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:143137200-143138800	Enhancers	Brain Substantia Nigra	brain
7	chr3:143137200-143139000	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr3:143137200-143139200	Enhancers	Brain Cingulate Gyrus	brain
9	chr3:143137600-143142000	Weak transcription	Dnd41	blood
10	chr3:143137800-143138800	Weak transcription	Brain Angular Gyrus	brain
11	chr3:143138000-143138400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:143138200-143138800	Enhancers	Brain Hippocampus Middle	brain

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