Variant report

Variant	rs17602572
Chromosome Location	chr11:59948374-59948375
allele	C/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: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10897009	0.84[EUR][1000 genomes]
rs10897011	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11230147	0.89[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs11230153	0.83[EUR][1000 genomes]
rs11230155	0.84[EUR][1000 genomes]
rs11230160	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11230161	0.89[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap]
rs11230180	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11230183	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11230184	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1125357	0.81[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes]
rs1151104	0.89[CHB][hapmap]
rs11600716	0.89[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes]
rs11605427	0.93[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12226022	0.81[EUR][1000 genomes]
rs12453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1286169	0.89[CHB][hapmap]
rs1303615	0.82[CEU][hapmap]
rs1303621	0.82[CEU][hapmap]
rs1426250	0.81[CEU][hapmap]
rs1441586	0.82[CEU][hapmap]
rs17528859	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs17529983	0.82[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs1820430	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834549	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834550	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834551	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834557	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015475	0.81[CEU][hapmap]
rs2070970	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs2081545	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2123314	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165525	0.84[EUR][1000 genomes]
rs2278867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2583471	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs2583476	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2847655	0.89[CEU][hapmap]
rs2847663	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap]
rs2847666	0.89[CEU][hapmap]
rs2847668	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs2855017	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs28628869	0.83[ASN][1000 genomes]
rs28672915	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs474951	0.89[CHB][hapmap]
rs4939311	0.89[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes]
rs4939312	0.89[CEU][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs4939314	0.84[EUR][1000 genomes]
rs501697	0.89[CHB][hapmap]
rs502581	0.82[CEU][hapmap]
rs525794	0.82[CEU][hapmap]
rs528823	0.89[CHB][hapmap]
rs539360	0.89[CHB][hapmap]
rs540170	0.82[CEU][hapmap]
rs55847558	0.82[EUR][1000 genomes]
rs558678	0.89[CHB][hapmap]
rs558788	0.88[CHB][hapmap]
rs56189574	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56201148	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574695	0.82[CEU][hapmap]
rs579721	0.89[CHB][hapmap]
rs581133	0.82[CEU][hapmap]
rs583296	0.82[CEU][hapmap]
rs583791	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs606588	0.84[CEU][hapmap]
rs610932	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs61901691	0.80[EUR][1000 genomes]
rs624663	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs631853	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs632185	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs634475	0.86[EUR][1000 genomes]
rs636147	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs662196	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs7116190	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7124974	0.80[EUR][1000 genomes]
rs72918674	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7926344	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7926354	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7926729	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7926954	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7933202	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7933805	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7939882	0.84[EUR][1000 genomes]
rs7946992	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs920573	0.89[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes]
rs983392	0.80[EUR][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17602572	MS4A4A	cis	multi-tissue	Pritchard

Chromatin state (count:16 , 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	chr11:59944000-59950400	Weak transcription	GM12878-XiMat	blood
5	chr11:59944400-59949200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
6	chr11:59946600-59948800	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
7	chr11:59946800-59952000	Active TSS	Adipose Nuclei	Adipose
8	chr11:59947200-59948600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr11:59947600-59953000	Enhancers	Fetal Intestine Small	intestine
10	chr11:59947800-59949000	Active TSS	Right Atrium	heart
11	chr11:59947800-59950600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:59948000-59949000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr11:59948000-59949200	Weak transcription	Primary B cells from cord blood	blood
14	chr11:59948000-59950000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr11:59948200-59948400	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr11:59948200-59949000	Weak transcription	Brain Hippocampus Middle	brain

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