Variant report

Variant	rs1554486
Chromosome Location	chr12:74679054-74679055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10128762	0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs10161169	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10748253	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10785097	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10879739	0.83[AFR][1000 genomes]
rs10879745	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10879747	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11180024	0.83[AMR][1000 genomes]
rs11180030	0.81[AMR][1000 genomes]
rs1346247	0.82[AMR][1000 genomes]
rs1365538	0.82[AMR][1000 genomes]
rs1402968	0.83[AFR][1000 genomes]
rs1522127	0.83[AFR][1000 genomes]
rs1608084	0.83[AFR][1000 genomes]
rs2103017	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs476953	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4883509	0.87[EUR][1000 genomes]
rs524863	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs526964	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs575786	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58864603	0.83[AMR][1000 genomes]
rs606888	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs624394	0.92[CEU][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs626946	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs645007	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs673310	0.86[EUR][1000 genomes]
rs7397269	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7971189	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9943773	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039468	chr12:74080586-75000246	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv559396	chr12:74586210-74679054	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv520257	chr12:74590356-74680999	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1047574	chr12:74599663-74687663	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv469472	chr12:74651797-74690292	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv559411	chr12:74651797-74690292	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv899290	chr12:74666737-74729489	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv899291	chr12:74666737-74740958	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1051702	chr12:74674733-74732069	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv469473	chr12:74676381-74712896	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv559412	chr12:74676381-74712896	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	esv3497363	chr12:74677995-74679907	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
13	esv3497374	chr12:74677995-74679907	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv826437	chr12:74678108-74679673	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1554486	TPH2	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:74676200-74679200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:74678800-74679400	Weak transcription	K562	blood
3	chr12:74679000-74679200	Enhancers	HMEC	breast
4	chr12:74679000-74679400	Enhancers	Placenta	Placenta

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