Variant report

Variant	rs3809578
Chromosome Location	chr15:31394537-31394538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr15:31394131-31394721	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
TRPM1	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10152647	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11070810	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12906564	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12910440	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12914420	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12917436	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3826030	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493451	0.88[CEU][hapmap];0.84[CHD][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8040406	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9302157	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
5	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	esv33507	chr15:31183324-31471023	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv1052722	chr15:31261834-31609680	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv542315	chr15:31261834-31609680	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
10	nsv903836	chr15:31330280-31512652	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
11	nsv431372	chr15:31341461-31409090	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1040840	chr15:31348902-31412706	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
13	nsv542316	chr15:31348902-31412706	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
14	nsv1045872	chr15:31355383-31396605	Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
15	nsv568770	chr15:31356425-31394537	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
16	esv2761861	chr15:31356726-31395194	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
17	nsv903837	chr15:31362654-31418766	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv1046253	chr15:31364402-31412706	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv1050000	chr15:31370411-31396633	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv1044255	chr15:31391226-31424185	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3809578	SNORD116-21	cis	parietal	SCAN
rs3809578	TRPM1,MIR211	cis	brain	BrainEAC
rs3809578	TRPM1,MIR211	cis	intralobular white matter	BrainEAC
rs3809578	TRPM1,MIR211	cis	inferior olivary nucleus	BrainEAC
rs3809578	SCG5	cis	parietal	SCAN
rs3809578	TRPM1,MIR211	cis	hippocampus	BrainEAC
rs3809578	TRPM1,MIR211	cis	thalamus	BrainEAC
rs3809578	TRPM1,MIR211	cis	substantia nigra	BrainEAC

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31391000-31395600	Enhancers	Brain Hippocampus Middle	brain
2	chr15:31391400-31394600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:31391600-31396200	Weak transcription	Placenta	Placenta
4	chr15:31392200-31394600	Enhancers	Stomach Mucosa	stomach
5	chr15:31392200-31397200	Weak transcription	A549	lung
6	chr15:31392400-31396400	Weak transcription	GM12878-XiMat	blood
7	chr15:31392400-31396600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:31392600-31394800	Enhancers	Brain Substantia Nigra	brain
9	chr15:31392600-31398000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr15:31392800-31395400	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr15:31392800-31397200	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr15:31393200-31394800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:31393200-31395000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:31393200-31395400	Enhancers	Brain Angular Gyrus	brain
15	chr15:31393400-31395400	Enhancers	Esophagus	oesophagus
16	chr15:31393400-31395600	Enhancers	Brain Anterior Caudate	brain
17	chr15:31393400-31396600	Weak transcription	Fetal Kidney	kidney
18	chr15:31393600-31394600	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr15:31393600-31394600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:31393600-31395400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:31393800-31395400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr15:31394000-31395000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:31394000-31395000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:31394200-31395400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:31394400-31394600	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr15:31394400-31395600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:31394400-31397600	Weak transcription	Brain Germinal Matrix	brain

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