Variant report

Variant	rs10138180
Chromosome Location	chr14:72846806-72846807
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:72845757..72848710-chr14:72852431..72853988,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1072167	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12892244	0.82[JPT][hapmap]
rs1356843	0.80[TSI][hapmap]
rs1520331	0.96[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs1520332	0.96[CEU][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs2079504	0.80[TSI][hapmap]
rs2079505	0.80[TSI][hapmap]
rs2079506	0.80[TSI][hapmap]
rs2090737	0.92[CEU][hapmap]
rs2108361	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2108362	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2214965	0.82[TSI][hapmap]
rs2238199	0.88[CEU][hapmap]
rs2239224	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2239225	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2239229	0.80[MEX][hapmap];0.83[TSI][hapmap]
rs2239231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2239233	0.91[EUR][1000 genomes]
rs2239248	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2239249	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs2283385	0.80[MEX][hapmap]
rs2283390	0.96[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs2332829	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2332831	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2529460	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2529461	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2529466	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2681728	0.96[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs2681731	0.80[TSI][hapmap]
rs2681742	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs2681748	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2681749	0.83[TSI][hapmap]
rs2681754	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2681761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2681765	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2681767	0.80[TSI][hapmap]
rs2681768	0.80[TSI][hapmap]
rs4903013	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6574067	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6574068	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6574070	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6574071	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7146606	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7149872	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8022289	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs847326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs847327	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs847332	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs847333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs847354	0.82[TSI][hapmap]
rs929413	0.80[TSI][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
rs10138180	C14orf43	cis	cerebellum	SCAN
rs10138180	PCNX	cis	parietal	SCAN
rs10138180	C14orf115	cis	cerebellum	SCAN
rs10138180	TMED10	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72836000-72851400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:72846800-72848000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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