Variant report

Variant	rs12065389
Chromosome Location	chr1:90971259-90971260
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10493838	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10801817	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10922869	0.92[EUR][1000 genomes]
rs10922870	0.92[EUR][1000 genomes]
rs11484926	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12061177	0.91[EUR][1000 genomes]
rs12064691	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094515	0.91[EUR][1000 genomes]
rs1336874	0.92[EUR][1000 genomes]
rs1336881	0.81[EUR][1000 genomes]
rs1893672	0.91[EUR][1000 genomes]
rs1954970	0.92[EUR][1000 genomes]
rs535756	0.96[EUR][1000 genomes]
rs58754941	1.00[ASN][1000 genomes]
rs59996763	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658710	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684834	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs693530	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525937	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7533106	0.95[EUR][1000 genomes]
rs885141	0.91[EUR][1000 genomes]
rs954472	0.91[EUR][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	esv3394726	chr1:90811671-91019675	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv1801569	chr1:90819992-90983299	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	esv1808806	chr1:90819992-90983299	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	esv1822918	chr1:90819992-90983299	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	esv1850863	chr1:90819992-90983299	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	esv2757740	chr1:90819992-90983299	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	esv2758949	chr1:90819992-90983299	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv427697	chr1:90819992-90983299	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv428124	chr1:90819992-90983299	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	esv1811797	chr1:90819992-91008105	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12065389	BTBD8	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:90966800-90974800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:90968000-90975000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:90968600-90973800	Weak transcription	Stomach Mucosa	stomach
4	chr1:90968800-90974200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:90969800-90971800	Enhancers	Dnd41	blood

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