Variant report

Variant	rs12461941
Chromosome Location	chr19:37984650-37984651
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11083427	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11083428	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11083430	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1128327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666662	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11666738	0.90[JPT][hapmap]
rs12151218	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151280	0.90[JPT][hapmap]
rs12162238	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12459013	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12459975	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12460230	0.90[JPT][hapmap]
rs12462271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12462505	1.00[JPT][hapmap]
rs12462524	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12986074	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs12986146	0.90[JPT][hapmap]
rs17243355	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17303301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279150	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2290999	0.90[JPT][hapmap]
rs35014847	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35205379	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3745764	0.89[ASW][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.89[MKK][hapmap]
rs3826849	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs7248397	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057688	chr19:37828019-37988253	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv833819	chr19:37899501-38051599	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1056753	chr19:37963714-38015943	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12461941	CATSPERG	cis	parietal	SCAN
rs12461941	PSMC4	cis	parietal	SCAN
rs12461941	FOSB	cis	cerebellum	SCAN
rs12461941	CEACAM19	cis	cerebellum	SCAN
rs12461941	MRPS12	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37963800-37985600	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr19:37984000-37984800	ZNF genes & repeats	Liver	Liver
3	chr19:37984400-37984800	ZNF genes & repeats	Primary T cells from cord blood	blood
4	chr19:37984400-37984800	ZNF genes & repeats	Brain Substantia Nigra	brain
5	chr19:37984400-37984800	ZNF genes & repeats	Fetal Brain Male	brain
6	chr19:37984400-37984800	ZNF genes & repeats	Fetal Heart	heart
7	chr19:37984400-37984800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle

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