Variant report

Variant	rs2190508
Chromosome Location	chr14:72834466-72834467
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	chr14:72829562..72831650-chr14:72833232..72835996,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10129799	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10137579	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10138152	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10149207	0.86[CEU][hapmap]
rs1072166	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1099968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1356841	0.82[EUR][1000 genomes]
rs1356843	0.83[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs1812041	0.88[EUR][1000 genomes]
rs1915132	0.86[EUR][1000 genomes]
rs2079504	0.83[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs2079505	0.83[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs2079506	0.83[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2176841	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2214965	0.86[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2239229	0.90[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2239230	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2239232	0.88[EUR][1000 genomes]
rs2239234	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs2239235	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs2239238	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs2239239	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs2239241	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs2239243	0.87[EUR][1000 genomes]
rs2247090	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs2283385	0.90[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283388	0.85[EUR][1000 genomes]
rs2332832	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2529457	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2529467	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2529468	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2529469	0.83[CEU][hapmap]
rs2529470	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs2529471	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs2681727	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs2681730	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs2681731	0.83[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs2681733	0.92[EUR][1000 genomes]
rs2681734	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs2681735	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs2681736	0.95[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs2681737	0.82[EUR][1000 genomes]
rs2681741	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs2681743	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs2681744	0.88[EUR][1000 genomes]
rs2681745	0.88[EUR][1000 genomes]
rs2681747	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2681749	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2681751	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2681752	1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2681753	0.87[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2681754	0.80[ASW][hapmap]
rs2681757	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2681767	0.83[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2681768	0.83[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs2681769	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs2681771	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs2877805	0.83[CEU][hapmap]
rs34582179	0.81[EUR][1000 genomes]
rs4903013	0.84[YRI][hapmap]
rs6574067	0.84[YRI][hapmap]
rs6574071	0.90[ASW][hapmap];0.80[MEX][hapmap]
rs7140973	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7150465	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7151325	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8003559	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs8003591	0.87[EUR][1000 genomes]
rs8015917	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs8016720	0.82[EUR][1000 genomes]
rs8019358	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs8022859	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs8022956	0.87[EUR][1000 genomes]
rs886826	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs929413	0.83[CEU][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2190508	TMED10	cis	parietal	SCAN
rs2190508	C14orf43	cis	cerebellum	SCAN
rs2190508	C14orf115	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72833200-72834600	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr14:72834400-72835000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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