Variant report

Variant	rs12714199
Chromosome Location	chr2:86812549-86812550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr2:86812309-86812661	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000252453	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1015117	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10169746	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10184584	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10184879	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs10184985	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10187880	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10188515	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1020306	0.81[ASN][1000 genomes]
rs1030887	0.80[YRI][hapmap]
rs10432704	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1080551	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11127046	0.93[ASN][1000 genomes]
rs11127047	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1137684	0.81[ASN][1000 genomes]
rs11676576	0.93[ASN][1000 genomes]
rs11684230	0.81[ASN][1000 genomes]
rs11689330	1.00[ASN][1000 genomes]
rs11689593	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12328637	0.84[ASN][1000 genomes]
rs12613282	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12614447	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12615285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12623509	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs12714188	0.93[ASN][1000 genomes]
rs12714190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714198	0.94[JPT][hapmap]
rs12987172	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12991654	1.00[ASN][1000 genomes]
rs13015620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13034615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13390713	0.93[ASN][1000 genomes]
rs13408041	0.92[ASN][1000 genomes]
rs13429696	0.93[ASN][1000 genomes]
rs1518807	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1629293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17027296	0.80[YRI][hapmap]
rs218059	0.93[ASN][1000 genomes]
rs2241803	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2367546	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs308900	0.82[ASN][1000 genomes]
rs3201448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs34666164	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731812	0.81[ASN][1000 genomes]
rs3755002	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs422240	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4832040	0.92[ASN][1000 genomes]
rs4832042	0.99[ASN][1000 genomes]
rs4832043	0.82[ASN][1000 genomes]
rs4832045	0.97[ASN][1000 genomes]
rs4832296	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4832297	0.93[ASN][1000 genomes]
rs4832299	0.85[ASN][1000 genomes]
rs4832300	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4832302	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832304	0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs62147239	0.99[ASN][1000 genomes]
rs6728211	0.97[ASN][1000 genomes]
rs6731025	0.87[ASN][1000 genomes]
rs6738663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6740863	0.80[YRI][hapmap]
rs6750226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6752371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7369138	0.81[ASN][1000 genomes]
rs7557796	0.96[CEU][hapmap];0.88[CHB][hapmap]
rs7568840	0.96[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7570640	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7587034	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7593151	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7596717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7601115	0.84[ASN][1000 genomes]
rs8179729	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9284788	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription 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 miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12714199	VPS24	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86810200-86812600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:86810400-86812600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr2:86810600-86812600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:86810600-86812600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:86810800-86812600	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr2:86811000-86812600	Enhancers	Primary hematopoietic stem cells	blood
7	chr2:86811000-86812600	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr2:86811400-86812800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:86811600-86812600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr2:86811600-86812800	Enhancers	HUVEC	blood vessel
11	chr2:86811800-86812600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr2:86812000-86813800	Weak transcription	Dnd41	blood
13	chr2:86812000-86814200	Weak transcription	K562	blood

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