Variant report

Variant	rs1488933
Chromosome Location	chr11:17267029-17267030
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs105290	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10741724	0.83[ASN][1000 genomes]
rs10766381	0.91[ASN][1000 genomes]
rs10766382	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832733	0.92[CHD][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap]
rs10832745	0.89[ASN][1000 genomes]
rs10832746	0.89[ASN][1000 genomes]
rs10832747	0.86[YRI][hapmap];0.89[ASN][1000 genomes]
rs10832748	0.83[ASN][1000 genomes]
rs10832750	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024148	0.86[JPT][hapmap];0.88[YRI][hapmap]
rs11024158	0.96[CHD][hapmap];0.86[JPT][hapmap]
rs11024204	0.92[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.89[ASN][1000 genomes]
rs11024207	0.91[ASN][1000 genomes]
rs11024208	0.91[ASN][1000 genomes]
rs11024220	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024221	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024223	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024229	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024231	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1125737	0.85[ASN][1000 genomes]
rs12276859	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12280930	0.86[JPT][hapmap];0.88[YRI][hapmap]
rs12286505	0.86[JPT][hapmap];0.87[YRI][hapmap]
rs190046	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1979603	0.91[ASN][1000 genomes]
rs214067	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs214069	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs214071	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs214075	0.94[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs214076	0.94[ASW][hapmap];0.84[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs214079	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs214081	0.84[ASN][1000 genomes]
rs214082	0.92[CHB][hapmap];0.83[CHD][hapmap];0.84[ASN][1000 genomes]
rs214083	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs214084	0.84[ASN][1000 genomes]
rs214085	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs214087	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs214088	0.84[ASN][1000 genomes]
rs214092	0.91[CHB][hapmap];0.83[CHD][hapmap];0.84[ASN][1000 genomes]
rs214093	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs214094	0.83[ASN][1000 genomes]
rs214095	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs214097	0.92[CHB][hapmap];0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs214099	0.83[ASN][1000 genomes]
rs214101	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs214102	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs214900	0.96[CHD][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs214901	0.96[CHD][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs214902	0.87[EUR][1000 genomes]
rs214904	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs214907	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs214909	0.86[ASN][1000 genomes]
rs214910	0.92[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.86[ASN][1000 genomes]
rs214913	0.84[ASN][1000 genomes]
rs214914	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs214915	0.86[ASN][1000 genomes]
rs214916	0.86[ASN][1000 genomes]
rs214917	0.81[ASN][1000 genomes]
rs214918	0.86[ASN][1000 genomes]
rs214919	0.86[ASN][1000 genomes]
rs214920	0.86[ASN][1000 genomes]
rs214921	0.86[ASN][1000 genomes]
rs214922	0.86[ASN][1000 genomes]
rs214923	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs214925	0.92[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.84[ASN][1000 genomes]
rs214926	0.80[ASN][1000 genomes]
rs214927	0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs214933	0.83[CHB][hapmap];0.96[CHD][hapmap]
rs214935	0.86[JPT][hapmap];0.88[YRI][hapmap]
rs214936	0.96[CHD][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap]
rs214939	0.86[JPT][hapmap];0.92[YRI][hapmap]
rs214940	0.96[CHD][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap]
rs2171615	0.83[ASN][1000 genomes]
rs4356203	0.83[CHD][hapmap]
rs4508187	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4509731	0.88[ASN][1000 genomes]
rs512852	0.86[JPT][hapmap];0.88[YRI][hapmap]
rs550667	0.84[YRI][hapmap]
rs567033	0.81[EUR][1000 genomes]
rs603618	0.92[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.89[ASN][1000 genomes]
rs61357262	0.85[ASN][1000 genomes]
rs615358	0.86[JPT][hapmap]
rs618331	0.92[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.89[ASN][1000 genomes]
rs677042	0.81[EUR][1000 genomes]
rs677540	0.96[CHD][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap]
rs7101686	0.84[ASN][1000 genomes]
rs7108315	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7108316	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7118443	0.83[ASN][1000 genomes]
rs7123301	0.96[CHD][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap]
rs7125607	0.86[JPT][hapmap];0.88[YRI][hapmap]
rs7128822	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7342262	0.92[CHB][hapmap];0.84[YRI][hapmap];0.91[ASN][1000 genomes]
rs7925692	0.83[ASW][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7927240	0.86[JPT][hapmap]
rs7937176	0.92[YRI][hapmap];0.93[ASN][1000 genomes]
rs7938820	0.86[JPT][hapmap];0.84[YRI][hapmap]
rs7940253	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7949699	0.91[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][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	nsv467711	chr11:17027555-17320797	Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv553568	chr11:17027555-17320797	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv469762	chr11:17170690-17320691	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv482905	chr11:17170690-17320691	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1488933	NUCB2	cis	Lymphoblastoid	GTEx
rs1488933	OR7E14P	cis	Esophagus Mucosa	GTEx
rs1488933	TMEM86A	cis	parietal	SCAN
rs1488933	NUCB2	Cis_1M	lymphoblastoid	RTeQTL
rs1488933	NUCB2	cis	multi-tissue	Pritchard
rs1488933	ZDHHC13	cis	cerebellum	SCAN
rs1488933	GTF2H1	cis	cerebellum	SCAN
rs1488933	OR7E14P	cis	Nerve Tibial	GTEx
rs1488933	NUCB2	cis	lymphoblastoid	seeQTL
rs1488933	MRGPRX1	cis	cerebellum	SCAN
rs1488933	NUCB2	cis	cerebellum	SCAN
rs1488933	SERGEF	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17265000-17267200	Enhancers	Dnd41	blood
2	chr11:17265600-17267200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr11:17266400-17267400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr11:17267000-17278800	Weak transcription	Primary T cells from cord blood	blood

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