Variant report

Variant	rs583791
Chromosome Location	chr11:59947252-59947253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MS4A4E-1	chr11:59946964-59949214	NONHSAT021562

Extended variants
information (count: 73 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs107903	0.93[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10897011	0.83[EUR][1000 genomes]
rs11230180	0.83[EUR][1000 genomes]
rs1125357	0.81[CEU][hapmap]
rs11605427	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs12453	0.89[CEU][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs1303615	0.83[ASW][hapmap];0.93[CEU][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs1303621	0.93[CEU][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs1441586	0.93[CEU][hapmap];0.89[JPT][hapmap]
rs17529983	0.81[CEU][hapmap]
rs17602572	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1820430	0.83[EUR][1000 genomes]
rs1834549	0.83[EUR][1000 genomes]
rs1834550	0.83[EUR][1000 genomes]
rs1834551	0.83[EUR][1000 genomes]
rs1834557	0.82[EUR][1000 genomes]
rs2081545	0.83[EUR][1000 genomes]
rs2278867	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs2847663	0.85[CEU][hapmap]
rs2847667	0.88[CEU][hapmap]
rs476722	0.93[CEU][hapmap];0.89[JPT][hapmap]
rs483629	0.84[EUR][1000 genomes]
rs502419	0.93[CEU][hapmap];0.89[JPT][hapmap]
rs502581	0.93[CEU][hapmap];0.89[JPT][hapmap]
rs504272	0.84[EUR][1000 genomes]
rs510518	0.84[EUR][1000 genomes]
rs512495	0.81[EUR][1000 genomes]
rs514266	0.83[EUR][1000 genomes]
rs516478	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs521952	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs525794	0.93[CEU][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.84[EUR][1000 genomes]
rs534273	0.84[EUR][1000 genomes]
rs540170	0.93[CEU][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs555635	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs556917	0.93[CEU][hapmap];0.89[JPT][hapmap]
rs56201148	0.83[EUR][1000 genomes]
rs563803	0.83[EUR][1000 genomes]
rs564912	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs569046	0.92[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs574695	0.93[CEU][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs574704	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs574798	0.83[EUR][1000 genomes]
rs580064	0.82[CEU][hapmap]
rs581133	0.93[CEU][hapmap];0.89[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs583296	0.93[CEU][hapmap];0.89[JPT][hapmap]
rs595481	0.92[CEU][hapmap]
rs602396	0.93[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs606588	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs610932	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs617135	0.85[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs617916	0.92[CEU][hapmap];0.88[JPT][hapmap]
rs624663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs631853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs632185	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs634475	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs636147	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs652354	0.89[CEU][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs662196	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs667897	0.85[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs684961	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs688030	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs72918674	0.86[EUR][1000 genomes]
rs7926344	0.81[EUR][1000 genomes]
rs7926354	0.81[EUR][1000 genomes]
rs7926729	0.81[EUR][1000 genomes]
rs7926954	0.82[EUR][1000 genomes]
rs7933202	0.89[CEU][hapmap]
rs7935829	0.89[CEU][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs7946992	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	nsv468579	chr11:59814287-59975400	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv555150	chr11:59814287-59975400	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv832174	chr11:59909267-60073908	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv524137	chr11:59936979-59947252	Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs583791	SNORD27	cis	cerebellum	SCAN
rs583791	GNG3	cis	parietal	SCAN
rs583791	SLC43A3	cis	parietal	SCAN
rs583791	FAM111A	cis	parietal	SCAN
rs583791	MTA2	cis	cerebellum	SCAN
rs583791	FRY	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59937200-59949800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr11:59942600-59949200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr11:59943600-59948600	Weak transcription	Liver	Liver
4	chr11:59943800-59947600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr11:59944000-59950400	Weak transcription	GM12878-XiMat	blood
6	chr11:59944400-59949200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
7	chr11:59946600-59948000	Enhancers	Primary B cells from cord blood	blood
8	chr11:59946600-59948800	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
9	chr11:59946800-59952000	Active TSS	Adipose Nuclei	Adipose
10	chr11:59947000-59947400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr11:59947200-59948200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
12	chr11:59947200-59948200	Active TSS	Brain Hippocampus Middle	brain
13	chr11:59947200-59948600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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