Variant report

Variant	rs12500557
Chromosome Location	chr4:130051748-130051749
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:130049431..130052409-chr4:130054376..130057821,3	K562	blood:
2	chr4:130036050..130038012-chr4:130049891..130052657,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1030830	0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs10494317	0.84[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap]
rs12500341	0.85[CHB][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap]
rs12503465	0.80[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs12504200	0.81[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs12505207	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12512345	0.81[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap]
rs12512846	0.97[ASN][1000 genomes]
rs17185550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17185620	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17416188	0.81[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap]
rs17416706	0.81[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs1756011	0.95[YRI][hapmap]
rs1877836	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs189236	0.85[YRI][hapmap]
rs1900397	0.81[CEU][hapmap];0.85[CHB][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs2044523	0.81[CEU][hapmap];0.90[CHB][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs35162842	0.98[ASN][1000 genomes]
rs4533782	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4635829	0.95[ASN][1000 genomes]
rs4975191	0.81[CEU][hapmap];0.85[CHB][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap]
rs4975294	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4975302	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975304	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4975305	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs530686	0.85[AFR][1000 genomes]
rs6835359	0.80[JPT][hapmap]
rs6838427	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6840353	0.80[JPT][hapmap]
rs6847784	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs72685402	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72687104	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs921375	0.81[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs921377	0.85[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12500557	FLJ30655	cis	multi-tissue	Pritchard
rs12500557	HSPA4L	cis	parietal	SCAN
rs12500557	PHF17	cis	multi-tissue	Pritchard
rs12500557	LOC132321	cis	multi-tissue	Pritchard
rs12500557	ADRB3	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:130032400-130052200	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links