Variant report

Variant	rs12140603
Chromosome Location	chr1:171842811-171842812
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10914141	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12121064	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12123334	1.00[CHB][hapmap]
rs12123946	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12130277	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12134649	0.88[ASN][1000 genomes]
rs12136630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12140482	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12141865	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12143501	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12145177	1.00[CHB][hapmap]
rs2421949	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3817923	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6673009	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs74126507	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74126515	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74126524	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74126528	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7543247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv831893	chr1:171802450-171985000	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12140603	FMO9P	cis	cerebellum	SCAN
rs12140603	LOC646870	cis	parietal	SCAN
rs12140603	SNORD79	cis	cerebellum	SCAN
rs12140603	DNM3	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171828400-171850800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:171838800-171848200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:171839000-171844400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:171840600-171846200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:171841200-171846800	Weak transcription	Brain Substantia Nigra	brain
6	chr1:171841400-171846600	Weak transcription	Brain Angular Gyrus	brain
7	chr1:171841800-171846600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:171841800-171846600	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:171841800-171846600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:171841800-171846800	Weak transcription	Brain Anterior Caudate	brain
11	chr1:171842000-171846600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:171842000-171846800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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