Variant report

Variant	rs2254521
Chromosome Location	chr12:41873086-41873087
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:41867305..41870215-chr12:41872382..41875248,2	K562	blood:

Variant related genes	Relation type
ENSG00000257228	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10880077	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12298084	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299762	0.88[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.99[EUR][1000 genomes]
rs12313532	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314473	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322329	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12423463	1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs12424813	1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs12817240	1.00[ASN][1000 genomes]
rs12826427	1.00[ASN][1000 genomes]
rs12826692	1.00[ASN][1000 genomes]
rs12828934	1.00[ASN][1000 genomes]
rs2446145	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2608698	0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2608699	0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2608713	1.00[ASW][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730812	0.83[GIH][hapmap];1.00[MEX][hapmap]
rs2730815	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730825	0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2733288	1.00[ASW][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285559	0.83[GIH][hapmap];1.00[MEX][hapmap]
rs285571	0.83[GIH][hapmap]
rs285588	1.00[MEX][hapmap]
rs285596	0.83[GIH][hapmap];1.00[MEX][hapmap]
rs287087	0.83[GIH][hapmap];1.00[MEX][hapmap]
rs34753427	1.00[ASN][1000 genomes]
rs35366617	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35487549	1.00[ASN][1000 genomes]
rs7133340	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]

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	nsv832384	chr12:41772648-41971430	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3337301	chr12:41851654-42093677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2627708	chr12:41872658-41874071	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2254521	PDZRN4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41869600-41905200	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:41871200-41873200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:41872800-41874000	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr12:41872800-41874400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:41873000-41873600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr12:41873000-41873800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr12:41873000-41874000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr12:41873000-41874000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr12:41873000-41874200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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