Variant report

Variant	rs1258246
Chromosome Location	chr10:50935160-50935161
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11101218	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1125165	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12265707	0.80[ASN][1000 genomes]
rs1258168	0.92[CEU][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1258169	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1258170	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1258176	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1258178	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1258179	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1258181	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1258182	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1258184	0.81[CEU][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1258201	0.89[JPT][hapmap]
rs1258204	0.89[JPT][hapmap];0.80[MKK][hapmap]
rs1258228	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1258241	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap]
rs1258243	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258245	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258247	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258249	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1258250	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1258251	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1258252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1258253	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1258255	0.86[EUR][1000 genomes]
rs1258256	0.96[CEU][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1258258	0.92[CEU][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1258260	0.92[CEU][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1258323	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1258326	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1258329	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1258330	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1268722	0.92[CEU][hapmap];0.82[GIH][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1268723	0.92[CEU][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1270562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1271629	0.88[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13736	0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs1625258	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1659305	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1992238	0.83[ASN][1000 genomes]
rs2377780	0.80[ASN][1000 genomes]
rs2889729	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4372365	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56948641	0.82[EUR][1000 genomes]
rs61846862	0.83[ASN][1000 genomes]
rs61846864	0.83[ASN][1000 genomes]
rs61846865	0.80[ASN][1000 genomes]
rs6537552	0.81[GIH][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6816	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7069682	0.80[ASN][1000 genomes]
rs7100934	0.83[ASN][1000 genomes]
rs745836	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs745837	0.92[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs745838	0.92[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7916489	0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv3346476	chr10:50610853-50987802	Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv3385048	chr10:50610942-50988537	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1037405	chr10:50800817-50940545	Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv895378	chr10:50801342-50955649	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1048905	chr10:50928727-51019190	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1258246	DRGX	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50927800-50940600	Weak transcription	Liver	Liver
2	chr10:50934800-50935400	ZNF genes & repeats	Fetal Brain Female	brain
3	chr10:50934800-50944000	Weak transcription	Brain Angular Gyrus	brain
4	chr10:50935000-50935200	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell

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