Variant report

Variant	rs1390939
Chromosome Location	chr8:20040712-20040713
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	EP300	chr8:20040486-20041008	SK-N-SH_RA	brain:	n/a	n/a
2	EP300	chr8:20039929-20041433	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr8:20040447-20041225	SH-SY5Y	brain:	n/a	chr8:20040872-20040893 chr8:20040876-20040886 chr8:20040879-20040888
4	GATA2	chr8:20040506-20041139	SH-SY5Y	brain:	n/a	chr8:20040872-20040893 chr8:20040876-20040886 chr8:20040879-20040888
5	YY1	chr8:20040579-20041087	SK-N-SH_RA	brain:	n/a	n/a
6	MXI1	chr8:20040009-20041539	SK-N-SH	brain:	n/a	n/a
7	EP300	chr8:20040507-20041006	SK-N-SH_RA	brain:	n/a	n/a
8	POLR2A	chr8:20040504-20040904	H1-neurons	neurons:	n/a	n/a
9	REST	chr8:20040523-20040958	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr8:20040492-20040917	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
SLC18A1	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11987726	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12549837	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12549838	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13269955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1390937	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs1497022	0.83[CHD][hapmap]
rs1532446	0.93[EUR][1000 genomes]
rs17411775	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs1813640	0.94[EUR][1000 genomes]
rs1908809	0.92[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs2018681	0.93[EUR][1000 genomes]
rs2270638	0.83[ASW][hapmap];0.83[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2270641	0.83[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2270642	0.83[ASW][hapmap];0.83[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2270645	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279708	0.92[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs2279709	0.92[CEU][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs2410637	0.83[ASN][1000 genomes]
rs55806365	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57312342	0.84[ASN][1000 genomes]
rs58116035	0.83[ASN][1000 genomes]
rs6586897	0.92[CEU][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs66504353	0.84[ASN][1000 genomes]
rs67315468	0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs67342356	0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs67679930	0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs721950	0.83[ASW][hapmap];0.83[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs73214045	0.82[ASN][1000 genomes]
rs73214052	0.84[ASN][1000 genomes]
rs73214054	0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv610759	chr8:19561997-20068842	Enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1033511	chr8:19751299-20625091	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv530877	chr8:19873053-20593254	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1015598	chr8:19963102-20088510	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv539523	chr8:19963102-20088510	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1390939	SLC18A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:20017400-20040800	Weak transcription	Fetal Intestine Small	intestine
2	chr8:20036000-20044200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr8:20040200-20041200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr8:20040400-20041000	Enhancers	Liver	Liver
5	chr8:20040400-20041000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
6	chr8:20040400-20041200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr8:20040600-20040800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr8:20040600-20041000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr8:20040600-20041000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr8:20040600-20041200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:20040600-20041400	Enhancers	Fetal Intestine Large	intestine

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