Variant report

Variant	rs5484
Chromosome Location	chr12:21531437-21531438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:21526910..21529766-chr12:21530369..21533433,3	K562	blood:
2	chr12:21528193..21534017-chr12:21534075..21538760,6	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1056007	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11834359	0.93[CEU][hapmap]
rs12300126	0.93[CEU][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12305367	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12306121	0.92[CEU][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs12308285	0.81[EUR][1000 genomes]
rs12317073	0.98[EUR][1000 genomes]
rs12319824	0.93[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12811082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12826226	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12826421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12833409	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17680787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213208	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs34417126	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34996992	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4762700	0.93[CEU][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4762701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.97[ASN][1000 genomes]
rs4762821	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304919	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7964783	0.86[CEU][hapmap];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv557735	chr12:21443282-21538957	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv469161	chr12:21507702-21555691	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv557737	chr12:21507702-21555691	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1040888	chr12:21522271-21568550	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv557738	chr12:21525704-21531437	Weak transcription Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv557739	chr12:21526472-21543215	Enhancers ZNF genes & repeats Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv519603	chr12:21526472-21584709	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv470274	chr12:21531437-21568050	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5484	LST-3TM12	cis	cerebellum	SCAN
rs5484	PLEKHA5	cis	parietal	SCAN
rs5484	PYROXD1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21527400-21532200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr12:21531400-21532200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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