Variant report

Variant	rs687476
Chromosome Location	chr1:216327410-216327411
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11120735	0.87[TSI][hapmap]
rs17597445	1.00[CHB][hapmap]
rs17649639	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs17651066	0.94[MKK][hapmap]
rs1830857	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[AFR][1000 genomes]
rs2926178	1.00[CHB][hapmap];0.94[MKK][hapmap]
rs301743	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301748	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs301749	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs301751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs301753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs301756	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs301757	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs301758	1.00[CHB][hapmap]
rs3106400	1.00[CHB][hapmap]
rs368107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371947	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs386851	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap]
rs400358	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs403340	1.00[CHB][hapmap]
rs414373	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs440921	1.00[AFR][1000 genomes]
rs446247	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs448588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449118	1.00[CHB][hapmap]
rs452747	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs453273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471271	1.00[CHB][hapmap]
rs532342	1.00[CHD][hapmap]
rs551629	0.82[AMR][1000 genomes]
rs551895	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56222536	1.00[AFR][1000 genomes]
rs594799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs619803	0.83[MKK][hapmap];0.86[ASN][1000 genomes]
rs627143	0.87[EUR][1000 genomes]
rs637374	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs656949	1.00[CHB][hapmap]
rs658740	1.00[CHB][hapmap]
rs676212	1.00[CEU][hapmap]
rs682319	1.00[CHB][hapmap];0.94[MKK][hapmap]
rs7413858	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[MKK][hapmap]
rs9729724	1.00[CHB][hapmap]

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	nsv1006504	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv535288	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv873176	chr1:216249570-216363137	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv999211	chr1:216268796-216329336	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1006028	chr1:216268796-216432545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs687476	TMEM206	cis	cerebellum	SCAN
rs687476	PINX1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216318800-216330400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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