Variant report

Variant	rs11904731
Chromosome Location	chr2:142885880-142885881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10496915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10496916	0.86[ASN][1000 genomes]
rs10928136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11695657	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349223	0.81[CHB][hapmap]
rs1449487	0.80[CHB][hapmap]
rs17831833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143778	0.86[ASN][1000 genomes]
rs61380612	0.86[ASN][1000 genomes]
rs62155641	0.86[ASN][1000 genomes]
rs62155642	0.86[ASN][1000 genomes]
rs969990	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[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	nsv997274	chr2:142760393-143599193	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv875254	chr2:142833327-142931146	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006247	chr2:142851056-143289465	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv979390	chr2:142883251-142888150	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11904731	HNMT	cis	parietal	SCAN
rs11904731	ZEB2	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142878200-142886800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr2:142879200-142887000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:142885000-142887600	Active TSS	Fetal Brain Female	brain
4	chr2:142885400-142886400	Enhancers	Fetal Brain Male	brain
5	chr2:142885400-142887400	Active TSS	Brain Cingulate Gyrus	brain
6	chr2:142885400-142890800	Active TSS	Brain Anterior Caudate	brain
7	chr2:142885600-142890400	Active TSS	Brain Substantia Nigra	brain
8	chr2:142885800-142886800	Enhancers	Hela-S3	cervix
9	chr2:142885800-142887600	Active TSS	Brain Hippocampus Middle	brain
10	chr2:142885800-142889800	Active TSS	Brain Angular Gyrus	brain
11	chr2:142885800-142890000	Active TSS	Brain Inferior Temporal Lobe	brain

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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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