Variant report

Variant	rs870675
Chromosome Location	chr1:62096235-62096236
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10736398	1.00[CHB][hapmap]
rs10789096	0.98[EUR][1000 genomes]
rs10889245	0.86[EUR][1000 genomes]
rs11207790	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11207791	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11207793	0.94[EUR][1000 genomes]
rs11207794	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12137416	0.96[EUR][1000 genomes]
rs12406569	0.99[EUR][1000 genomes]
rs12406599	1.00[EUR][1000 genomes]
rs12567173	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1390449	0.98[EUR][1000 genomes]
rs1933293	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1933294	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2029858	1.00[CHB][hapmap];0.84[MEX][hapmap]
rs35126542	0.99[EUR][1000 genomes]
rs59962858	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587935	0.98[EUR][1000 genomes]
rs6666322	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668107	0.88[EUR][1000 genomes]
rs6685530	0.93[EUR][1000 genomes]
rs6686620	0.87[EUR][1000 genomes]
rs6695578	0.98[EUR][1000 genomes]
rs6695763	0.98[EUR][1000 genomes]
rs6697976	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7517622	0.98[EUR][1000 genomes]
rs7518598	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7519731	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7519830	0.94[EUR][1000 genomes]
rs7528095	0.99[EUR][1000 genomes]
rs7542856	0.87[EUR][1000 genomes]
rs7542870	0.94[EUR][1000 genomes]
rs7551827	0.98[EUR][1000 genomes]
rs7554347	0.96[EUR][1000 genomes]
rs870674	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1006142	chr1:61696142-62119763	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv534980	chr1:61696142-62119763	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv916868	chr1:61700430-62119762	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv817402	chr1:61703965-62119762	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1010797	chr1:61703966-62125970	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1007318	chr1:62083960-62113102	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv1831777	chr1:62086216-62119201	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv508226	chr1:62091093-62140604	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs870675	TACSTD2	cis	cerebellum	SCAN
rs870675	USP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62073200-62098800	Weak transcription	Right Atrium	heart
2	chr1:62093400-62096400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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