Variant report

Variant	rs479333
Chromosome Location	chr2:32489158-32489159
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10172468	0.95[JPT][hapmap]
rs10208246	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs10490360	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11124275	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap]
rs11676938	0.89[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap]
rs11678119	0.82[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap]
rs11681731	0.80[EUR][1000 genomes]
rs12465351	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12614686	0.82[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.83[MKK][hapmap]
rs12617289	0.80[EUR][1000 genomes]
rs1265340	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1265341	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12997026	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs13022197	0.88[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.90[MKK][hapmap];0.91[YRI][hapmap];0.80[EUR][1000 genomes]
rs13427170	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs212678	0.80[EUR][1000 genomes]
rs212679	0.84[CEU][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs212687	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs212699	0.84[CEU][hapmap];0.80[LWK][hapmap]
rs212701	0.84[CEU][hapmap];0.80[LWK][hapmap]
rs212703	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs212715	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs212716	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs212717	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs212718	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs212721	0.87[GIH][hapmap];0.83[YRI][hapmap]
rs212723	0.81[EUR][1000 genomes]
rs212724	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs212725	0.82[EUR][1000 genomes]
rs212726	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs212727	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs212728	0.82[EUR][1000 genomes]
rs212730	0.94[CEU][hapmap];0.91[GIH][hapmap];0.82[LWK][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs212731	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs212735	0.82[EUR][1000 genomes]
rs212737	0.89[CEU][hapmap];0.82[LWK][hapmap];0.82[EUR][1000 genomes]
rs212738	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs212739	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs212744	0.95[JPT][hapmap]
rs212745	0.89[CEU][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs212746	0.89[CEU][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs212748	0.95[JPT][hapmap]
rs212755	0.84[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap]
rs212758	0.89[CEU][hapmap];0.83[GIH][hapmap]
rs212759	0.89[CEU][hapmap];0.83[GIH][hapmap];0.81[LWK][hapmap];0.83[YRI][hapmap]
rs212760	0.89[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs212762	1.00[JPT][hapmap]
rs216544	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap]
rs2235134	0.81[EUR][1000 genomes]
rs2280967	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap]
rs2366736	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2566483	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs374743	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3752916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs3769602	0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap]
rs3769604	0.82[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap]
rs3769606	0.89[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.87[YRI][hapmap]
rs385076	0.88[ASW][hapmap];0.89[CEU][hapmap];0.83[CHB][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs408813	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs428002	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs430759	0.84[CEU][hapmap];0.83[LWK][hapmap];0.83[YRI][hapmap]
rs435572	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.99[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs443609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs455060	0.94[CEU][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];0.82[EUR][1000 genomes]
rs466126	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs467523	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap]
rs472101	0.83[ASN][1000 genomes]
rs4952209	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs4952248	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs4952250	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs4952252	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs56861054	0.96[ASN][1000 genomes]
rs59966205	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62134033	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs659239	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6716179	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap]
rs6717209	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6723154	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.83[MKK][hapmap];0.83[YRI][hapmap]
rs6725184	0.82[ASW][hapmap];0.89[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.91[YRI][hapmap]
rs6758024	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6760105	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap]
rs7561519	0.89[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs7566162	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7572964	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs7573543	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.80[EUR][1000 genomes]
rs7581032	0.82[EUR][1000 genomes]
rs7581340	0.89[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs7581432	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs7588883	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs7605242	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv2422335	chr2:32412330-33200581	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	nsv2667	chr2:32444810-32489755	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv1002120	chr2:32470452-32539443	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1004279	chr2:32470452-32543369	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs479333	NLRC4	cis	lymphoblastoid	seeQTL
rs479333	EHD3	cis	parietal	SCAN
rs479333	NLRC4	cis	Lymphoblastoid	GTEx
rs479333	SLC30A6	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32486600-32489400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr2:32486800-32489200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr2:32487000-32489200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
4	chr2:32487000-32489600	Enhancers	Primary B cells from peripheral blood	blood
5	chr2:32487200-32490600	Active TSS	Primary hematopoietic stem cells	blood
6	chr2:32487400-32490600	Weak transcription	K562	blood
7	chr2:32487800-32489400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:32487800-32489600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:32488000-32489200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:32488200-32489200	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr2:32488400-32489600	Enhancers	HepG2	liver
12	chr2:32488400-32489800	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr2:32488600-32489200	Active TSS	Rectal Mucosa Donor 31	rectum
14	chr2:32489000-32489200	Flanking Active TSS	GM12878-XiMat	blood

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