Variant report

Variant	rs12666409
Chromosome Location	chr7:50634976-50634977
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	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: 34 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10249420	0.95[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs10265930	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs10271341	0.81[GIH][hapmap]
rs10276473	0.84[GIH][hapmap];0.82[TSI][hapmap]
rs10899748	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11238214	0.90[JPT][hapmap]
rs11489734	0.90[JPT][hapmap]
rs11575320	0.84[GIH][hapmap]
rs11976778	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12671598	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12673638	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470747	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs2329346	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2329371	0.84[GIH][hapmap];0.82[TSI][hapmap]
rs28415418	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3779078	0.84[GIH][hapmap]
rs3807556	0.84[GIH][hapmap];0.90[MKK][hapmap]
rs3807558	0.81[GIH][hapmap]
rs56105337	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56661863	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66792686	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68011952	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7779110	0.88[EUR][1000 genomes]
rs7790919	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7803440	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7803788	0.95[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs7803903	0.88[EUR][1000 genomes]
rs7807335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs978784	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12666409	FIGNL1	cis	parietal	SCAN
rs12666409	FIGNL1	cis	cerebellum	SCAN
rs12666409	FIGNL1	cis	Thyroid	GTEx
rs12666409	FIGNL1	cis	lung	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50620800-50635600	Weak transcription	Lung	lung
2	chr7:50633600-50635800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:50633800-50635200	Enhancers	Fetal Intestine Large	intestine
4	chr7:50633800-50635600	Enhancers	Fetal Intestine Small	intestine
5	chr7:50634200-50635600	Weak transcription	Liver	Liver
6	chr7:50634200-50635600	Weak transcription	Pancreas	Pancrea

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