Variant report

Variant	rs16846341
Chromosome Location	chr3:143094941-143094942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:143068671..143071346-chr3:143094512..143096094,2	K562	blood:
2	chr3:143089798..143091848-chr3:143094330..143096533,2	K562	blood:
3	chr3:143094103..143096377-chr3:143119769..143122751,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10513200	0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs10513201	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]
rs10935491	0.97[ASN][1000 genomes]
rs10935492	0.96[ASN][1000 genomes]
rs11707045	0.83[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs11707857	0.92[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs11719681	0.83[CHB][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs16853457	0.85[YRI][hapmap]
rs16853469	0.85[YRI][hapmap]
rs16853522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16853578	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]
rs17757146	0.83[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs17757182	0.96[ASN][1000 genomes]
rs1875459	0.83[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2360255	0.92[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs35233571	0.97[ASN][1000 genomes]
rs35358995	0.90[ASN][1000 genomes]
rs36125349	0.96[ASN][1000 genomes]
rs3860228	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs4311209	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4521222	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839634	0.83[JPT][hapmap]
rs56080141	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56152928	0.97[ASN][1000 genomes]
rs61301417	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770293	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6782465	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803041	0.80[JPT][hapmap]
rs73144740	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73144743	0.95[ASN][1000 genomes]
rs73144745	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73144749	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73144760	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73144769	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73144770	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73144771	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73144772	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73144773	0.97[ASN][1000 genomes]
rs73144774	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73144777	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7374585	0.90[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7617737	0.83[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7627844	0.96[ASN][1000 genomes]
rs7652087	0.83[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7652557	0.96[ASN][1000 genomes]
rs924576	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv877564	chr3:143059952-143116883	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv877565	chr3:143078986-143116883	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv999000	chr3:143086325-143136128	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16846341	PLSCR4	cis	parietal	SCAN
rs16846341	PLSCR4	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143071600-143102400	Weak transcription	Esophagus	oesophagus
2	chr3:143072000-143099400	Weak transcription	Ovary	ovary
3	chr3:143077400-143104800	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:143082400-143102200	Weak transcription	Primary B cells from cord blood	blood
5	chr3:143083000-143096600	Weak transcription	Primary T cells from cord blood	blood
6	chr3:143083200-143096000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:143083400-143098000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:143085800-143103200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:143088400-143096800	Weak transcription	Dnd41	blood
10	chr3:143088800-143099800	Weak transcription	Aorta	Aorta
11	chr3:143094000-143099400	Weak transcription	Spleen	Spleen
12	chr3:143094000-143099600	Weak transcription	Adipose Nuclei	Adipose
13	chr3:143094800-143095000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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