Variant report

Variant	rs1471712
Chromosome Location	chr11:47912150-47912151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10458915	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10742820	0.92[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10742824	0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10769299	0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10769300	0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838758	0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs10838759	0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs10838760	0.89[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs10838763	0.84[ASN][1000 genomes]
rs10838766	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10838767	0.84[ASN][1000 genomes]
rs10838768	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10838769	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10838771	0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10838773	0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10838774	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838775	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838776	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838777	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838782	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10838784	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10838786	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10838790	0.85[YRI][hapmap]
rs11039345	0.89[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap]
rs11039373	0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs11039376	0.83[ASN][1000 genomes]
rs11039377	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11039379	0.83[ASN][1000 genomes]
rs11039392	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039401	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11039402	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11039414	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039415	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039419	0.88[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039429	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039431	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039432	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039434	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11039467	0.85[JPT][hapmap]
rs12225854	0.83[ASN][1000 genomes]
rs12226431	0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12360643	0.82[ASN][1000 genomes]
rs12366244	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12421563	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12576933	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12785949	0.89[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs1563820	0.89[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1563821	0.89[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2046377	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125838	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2170815	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2290851	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs28617307	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2869541	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2904127	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2950888	0.84[YRI][hapmap]
rs3816605	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3886262	0.85[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4752792	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4752796	0.89[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4752798	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4752865	0.88[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60833259	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61895760	0.85[ASN][1000 genomes]
rs6485773	0.89[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs6485775	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6485778	0.83[ASN][1000 genomes]
rs6485786	0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6485794	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6485795	0.84[JPT][hapmap]
rs7101597	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7108479	0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7110300	0.88[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7111576	0.82[ASN][1000 genomes]
rs7111606	0.82[ASN][1000 genomes]
rs7112248	0.82[ASN][1000 genomes]
rs7113640	0.85[YRI][hapmap]
rs7114011	0.85[JPT][hapmap]
rs7114813	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7115228	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7116346	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7118747	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7121038	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7122182	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7122217	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7123952	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7124396	0.82[ASN][1000 genomes]
rs754434	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7925211	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7927445	0.85[JPT][hapmap]
rs7929014	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7929725	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7932703	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7933896	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7939420	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs7941399	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7943464	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7944084	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7948468	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7950674	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9633830	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1049835	chr11:47837089-47928822	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv541036	chr11:47837089-47928822	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv897326	chr11:47891334-48035474	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1471712	C1QTNF4	cis	multi-tissue	Pritchard
rs1471712		cis	Lymphoblastoid	GTEx
rs1471712	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs1471712	FNBP4	cis	lesional skin	skin_eQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47903200-47913400	Weak transcription	Hela-S3	cervix
2	chr11:47905400-47912400	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr11:47906000-47912200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr11:47906000-47912400	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr11:47906200-47912200	Enhancers	Primary T cells from cord blood	blood
6	chr11:47907800-47912400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr11:47907800-47913400	Weak transcription	NHDF-Ad	bronchial
8	chr11:47908000-47912200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:47908000-47912400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr11:47908200-47914600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:47909200-47912200	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr11:47911200-47912200	Enhancers	Primary B cells from peripheral blood	blood
13	chr11:47911200-47912200	Enhancers	Primary hematopoietic stem cells	blood
14	chr11:47911200-47912200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:47911200-47912200	Enhancers	Thymus	Thymus
16	chr11:47911200-47912200	Enhancers	HUVEC	blood vessel
17	chr11:47911200-47912400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:47911200-47912800	Enhancers	Primary B cells from cord blood	blood
19	chr11:47911400-47912200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr11:47911400-47912200	Enhancers	Adipose Nuclei	Adipose
21	chr11:47911400-47912200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr11:47911400-47912400	Enhancers	Primary T cells fromperipheralblood	blood

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