Variant report

Variant	rs11489734
Chromosome Location	chr7:50635730-50635731
allele	A/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	GATA3	chr7:50635487-50635743	SH-SY5Y	brain:	n/a	n/a
2	REST	chr7:50635370-50635975	SK-N-SH	brain:	n/a	n/a
3	EP300	chr7:50635340-50635803	SK-N-SH_RA	brain:	n/a	n/a
4	EP300	chr7:50635335-50635871	SK-N-SH_RA	brain:	n/a	n/a
5	GATA2	chr7:50635241-50635874	SH-SY5Y	brain:	n/a	n/a
6	EP300	chr7:50634186-50636749	SK-N-SH	brain:	n/a	chr7:50635005-50635019

Variant related genes	Relation type
DDC	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10238413	0.83[ASN][1000 genomes]
rs10274172	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10278338	0.84[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11238214	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238226	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11489736	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11977415	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12665904	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12666409	0.90[JPT][hapmap]
rs12669770	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1451375	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs1813214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1839740	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1966839	0.82[EUR][1000 genomes]
rs1987859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329340	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs2329342	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs3829897	0.80[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.80[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4275187	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4392851	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4452748	0.89[GIH][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs4469404	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4512339	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4601266	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947684	0.83[ASN][1000 genomes]
rs55718635	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55738142	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56233242	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59086818	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6593010	0.84[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68143668	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73125288	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73125290	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7797131	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7802148	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804365	0.86[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap]
rs7807335	0.90[JPT][hapmap]
rs921450	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs921451	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs978784	0.90[JPT][hapmap]

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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1032882	chr7:50611138-50775257	Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv538834	chr7:50611138-50775257	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11489734	FIGNL1	cis	lung	GTEx
rs11489734	FIGNL1	cis	parietal	SCAN
rs11489734	FIGNL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50633600-50635800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:50635600-50635800	Enhancers	Placenta	Placenta
3	chr7:50635600-50636000	Enhancers	Liver	Liver
4	chr7:50635600-50636000	Enhancers	Lung	lung

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