Variant report

Variant	rs2239249
Chromosome Location	chr14:72797361-72797362
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10138180	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs12894979	0.89[TSI][hapmap]
rs1356843	0.80[MEX][hapmap]
rs1402056	0.87[TSI][hapmap]
rs1520331	0.96[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs1520332	0.96[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs1996662	0.90[CHB][hapmap];0.85[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2079504	0.80[MEX][hapmap]
rs2079505	0.80[MEX][hapmap]
rs2079506	0.80[MEX][hapmap]
rs2090737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2238199	0.96[CEU][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2239224	0.92[CEU][hapmap]
rs2239231	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2239233	0.85[EUR][1000 genomes]
rs2239248	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2283390	0.96[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs2332829	0.82[EUR][1000 genomes]
rs2332831	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs2529460	0.80[EUR][1000 genomes]
rs2529461	0.80[EUR][1000 genomes]
rs2529466	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2681721	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2681728	0.96[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs2681731	0.80[MEX][hapmap]
rs2681736	0.80[MEX][hapmap]
rs2681742	0.96[CEU][hapmap];0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2681754	0.92[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2681761	0.95[CEU][hapmap]
rs2681765	0.80[EUR][1000 genomes]
rs2681767	0.80[MEX][hapmap]
rs2681768	0.80[MEX][hapmap]
rs4903003	0.89[TSI][hapmap]
rs4903013	0.81[CEU][hapmap]
rs6574067	0.81[CEU][hapmap]
rs6574071	0.81[CEU][hapmap]
rs847326	0.95[CEU][hapmap]
rs847327	0.96[CEU][hapmap]
rs847333	0.92[CEU][hapmap]
rs847347	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs847351	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs847352	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs847353	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs847354	0.89[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs847356	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap]
rs847357	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs929413	0.80[MEX][hapmap]

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	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv948800	chr14:72462557-73150701	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2239249	PCNX	cis	parietal	SCAN
rs2239249	C14orf115	cis	cerebellum	SCAN
rs2239249	TMED10	cis	parietal	SCAN
rs2239249	C14orf43	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72794400-72798200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr14:72794600-72797800	Weak transcription	Colon Smooth Muscle	Colon
3	chr14:72796400-72798200	Weak transcription	Lung	lung
4	chr14:72796400-72801000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr14:72796600-72799800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr14:72796600-72801400	Enhancers	Cortex derived primary cultured neurospheres	brain

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