Variant report

Variant	rs235893
Chromosome Location	chr1:171574772-171574773
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1055417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs10913167	1.00[CHB][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12136576	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12137832	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12139715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12142594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12145045	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12146022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap]
rs12734261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12759907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap]
rs171005	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183533	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs190198	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294292	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs2294293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs235471	0.80[ASN][1000 genomes]
rs235472	0.80[ASN][1000 genomes]
rs235488	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs235495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs235498	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235507	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235865	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235886	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235892	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235895	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235897	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs235898	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235899	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235900	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235901	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235902	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235903	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235904	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235910	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235911	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235912	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661007	1.00[ASN][1000 genomes]
rs46407	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536753	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559739	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591286	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs631259	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67133611	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71637418	0.80[ASN][1000 genomes]
rs71637419	0.80[ASN][1000 genomes]
rs7534464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7534557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7538745	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv3399610	chr1:171569794-171575719	Weak transcription Enhancers	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs235893	SELE	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171561800-171576600	Weak transcription	Brain Substantia Nigra	brain
2	chr1:171562200-171575600	Weak transcription	HepG2	liver
3	chr1:171569200-171576400	Weak transcription	GM12878-XiMat	blood
4	chr1:171570200-171575600	Weak transcription	Liver	Liver
5	chr1:171573200-171579600	Weak transcription	Adipose Nuclei	Adipose

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