Variant report

Variant	rs1770887
Chromosome Location	chr1:76401812-76401813
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr1:76401788-76401872	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ASB17	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10518521	0.80[EUR][1000 genomes]
rs10732723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs10873787	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873808	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873863	0.83[CEU][hapmap]
rs11161620	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap]
rs11161836	1.00[CEU][hapmap]
rs11161845	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161857	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1146646	1.00[CHB][hapmap];0.91[GIH][hapmap]
rs11588578	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1159214	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs12090849	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap]
rs12093623	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs12118399	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122939	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap]
rs1417405	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565717	0.87[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap]
rs1689275	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770885	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029681	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs2029683	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2172507	0.87[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap]
rs4949677	0.80[CEU][hapmap]
rs4949683	1.00[ASN][1000 genomes]
rs4949686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs5745336	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs5745427	0.87[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap]
rs5745433	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap]
rs5745442	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs5745449	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs61770550	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61770556	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61770557	1.00[ASN][1000 genomes]
rs6683437	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs6699682	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap]
rs7523573	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7547056	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap]
rs7549863	1.00[CHB][hapmap]
rs931507	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1004669	chr1:76301198-76409451	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1770887	MSH4	cis	parietal	SCAN
rs1770887	MSH4	cis	Esophagus Muscularis	GTEx
rs1770887	MSH4	cis	Artery Tibial	GTEx
rs1770887	SNORD45B	cis	parietal	SCAN
rs1770887	ACADM	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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