Variant report

Variant	rs12719151
Chromosome Location	chr5:112026480-112026481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:112025912..112028598-chr5:112039922..112042129,2	K562	blood:
2	chr5:112023980..112026718-chr5:112033004..112035530,2	K562	blood:
3	chr5:112024489..112026491-chr5:112028253..112031270,3	K562	blood:
4	chr5:112018990..112022293-chr5:112024063..112027716,5	K562	blood:
5	chr5:112023982..112026491-chr5:112028253..112030508,2	K562	blood:
6	chr5:112026203..112028934-chr5:112090617..112094558,3	K562	blood:
7	chr5:112025634..112029272-chr5:112039544..112043579,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134982	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10051624	0.80[EUR][1000 genomes]
rs10072068	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs10073398	0.86[EUR][1000 genomes]
rs10076641	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10463643	0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs10477483	0.84[EUR][1000 genomes]
rs11749632	0.90[EUR][1000 genomes]
rs11954856	0.81[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs12332692	0.83[EUR][1000 genomes]
rs12513804	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12659119	0.85[EUR][1000 genomes]
rs13156251	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs13173990	0.85[CEU][hapmap]
rs1441367	0.82[EUR][1000 genomes]
rs1441375	1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs1465910	0.85[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1530256	0.80[EUR][1000 genomes]
rs1661035	0.92[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs1661036	0.89[ASN][1000 genomes]
rs17285505	0.83[EUR][1000 genomes]
rs1816769	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1866924	0.82[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs1968557	0.80[EUR][1000 genomes]
rs2020383	0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs2099810	0.81[EUR][1000 genomes]
rs2289484	0.80[TSI][hapmap]
rs2431242	0.85[EUR][1000 genomes]
rs2439591	0.86[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs2900066	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2909786	0.85[CEU][hapmap]
rs2909787	0.85[CEU][hapmap]
rs2909958	0.81[CEU][hapmap]
rs35130225	0.85[EUR][1000 genomes]
rs351771	0.82[MEX][hapmap]
rs3846716	0.92[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs396321	0.80[CEU][hapmap]
rs4099181	0.81[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs41115	0.82[MEX][hapmap]
rs42427	0.82[MEX][hapmap]
rs464002	0.84[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs465899	0.82[MEX][hapmap]
rs468179	0.89[ASN][1000 genomes]
rs4705609	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4705815	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544243	0.92[GIH][hapmap];0.88[MEX][hapmap]
rs56335290	1.00[ASN][1000 genomes]
rs62364017	0.82[EUR][1000 genomes]
rs6594643	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6594644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6864688	0.86[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs6867243	0.87[EUR][1000 genomes]
rs6893949	0.86[EUR][1000 genomes]
rs6894351	0.85[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6898133	0.80[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7727738	0.80[EUR][1000 genomes]
rs861674	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9326862	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9326863	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs953916	0.90[EUR][1000 genomes]
rs971517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830450	chr5:111964170-112134510	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12719151	REEP5	cis	cerebellum	SCAN
rs12719151	NCRNA00219	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112021000-112026600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:112021000-112026600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:112021800-112030600	Weak transcription	Osteobl	bone
4	chr5:112022600-112030600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:112024200-112027200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr5:112024200-112027800	Enhancers	K562	blood
7	chr5:112025400-112026600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:112025600-112027000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:112026400-112027000	Enhancers	Cortex derived primary cultured neurospheres	brain

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