Variant report

Variant	rs10277662
Chromosome Location	chr7:50594836-50594837
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	chr7:50593552-50596619	SK-N-SH	brain:	n/a	chr7:50596383-50596393

Variant related genes	Relation type
ENSG00000226122	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10239830	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10249420	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10265930	0.84[ASN][1000 genomes]
rs10267323	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10271341	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10276473	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11575320	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11575463	0.91[EUR][1000 genomes]
rs11772714	0.89[EUR][1000 genomes]
rs12671474	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1376524	0.91[EUR][1000 genomes]
rs1470747	0.85[ASN][1000 genomes]
rs17733244	0.92[EUR][1000 genomes]
rs1807066	0.89[EUR][1000 genomes]
rs2044859	0.93[ASN][1000 genomes]
rs2060763	0.89[EUR][1000 genomes]
rs2329371	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2876828	0.90[EUR][1000 genomes]
rs2876829	0.92[EUR][1000 genomes]
rs28889020	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3735273	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3779074	0.93[ASN][1000 genomes]
rs3779078	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3807552	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3807555	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3807556	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3807558	0.91[EUR][1000 genomes]
rs6950777	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6963996	0.92[EUR][1000 genomes]
rs745042	0.89[EUR][1000 genomes]
rs745043	0.89[EUR][1000 genomes]
rs7776816	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7779110	0.87[ASN][1000 genomes]
rs7790758	0.92[EUR][1000 genomes]
rs7803440	0.87[ASN][1000 genomes]
rs7803788	0.87[ASN][1000 genomes]
rs7803903	0.87[ASN][1000 genomes]
rs880029	0.90[EUR][1000 genomes]
rs896309	0.90[EUR][1000 genomes]
rs9942686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv888021	chr7:50538589-50610071	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10277662	FIGNL1	cis	Heart Left Ventricle	GTEx
rs10277662	FIGNL1	cis	Thyroid	GTEx
rs10277662	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs10277662	FIGNL1	cis	Nerve Tibial	GTEx
rs10277662	FIGNL1	cis	Adipose Subcutaneous	GTEx
rs10277662	FIGNL1	cis	lung	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50543600-50595000	Weak transcription	Liver	Liver
2	chr7:50565200-50609000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr7:50582000-50595200	Weak transcription	Fetal Intestine Small	intestine
4	chr7:50584200-50595800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:50589000-50599200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:50589400-50595600	Strong transcription	Duodenum Mucosa	Duodenum
7	chr7:50592800-50595200	Strong transcription	HepG2	liver
8	chr7:50593400-50595800	Weak transcription	Fetal Intestine Large	intestine

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