Variant report

Variant	rs1224436
Chromosome Location	chr12:45400397-45400398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10880718	0.90[EUR][1000 genomes]
rs10880730	0.81[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs11182799	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs11182800	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11182802	0.82[CHB][hapmap]
rs11182810	0.85[EUR][1000 genomes]
rs11182811	0.86[EUR][1000 genomes]
rs1118481	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs11830299	0.80[ASN][1000 genomes]
rs1495033	0.84[EUR][1000 genomes]
rs1495034	0.90[EUR][1000 genomes]
rs1495035	0.94[EUR][1000 genomes]
rs1495036	0.94[EUR][1000 genomes]
rs1495042	0.81[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs1857924	0.83[EUR][1000 genomes]
rs1857925	0.83[EUR][1000 genomes]
rs1857926	0.89[EUR][1000 genomes]
rs2160987	0.82[CHB][hapmap]
rs2408140	0.92[EUR][1000 genomes]
rs2544102	0.89[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2643140	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs2731040	0.91[EUR][1000 genomes]
rs2731053	0.92[EUR][1000 genomes]
rs2731054	0.92[EUR][1000 genomes]
rs4285943	0.94[EUR][1000 genomes]
rs4561266	0.85[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs7963606	0.88[EUR][1000 genomes]
rs7964973	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899050	chr12:45299202-45400614	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	esv3351644	chr12:45345597-45529449	Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1045857	chr12:45351172-45468784	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv541485	chr12:45351172-45468784	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv469367	chr12:45363545-45400614	Enhancers Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv558753	chr12:45363545-45400614	Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1224436	CCL1	trans	cerebellum	SCAN
rs1224436	DBX2	cis	Skin Sun Exposed Lower leg	GTEx
rs1224436	NELL2	cis	Artery Tibial	GTEx
rs1224436	RP11-478B9.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45393000-45412600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:45394600-45406000	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links