Variant report

Variant	rs9942686
Chromosome Location	chr7:50596381-50596382
allele	A/G
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	SP1	chr7:50596370-50596817	HepG2	liver:	n/a	n/a
2	MAZ	chr7:50596172-50597032	HepG2	liver:	n/a	n/a
3	EP300	chr7:50593552-50596619	SK-N-SH	brain:	n/a	chr7:50596383-50596393
4	FOXA2	chr7:50596093-50596724	HepG2	liver:	n/a	n/a
5	SMC3	chr7:50596238-50596695	HepG2	liver:	n/a	n/a
6	HNF4A	chr7:50596360-50596812	HepG2	liver:	n/a	chr7:50596586-50596601 chr7:50596586-50596601 chr7:50596586-50596601 chr7:50596588-50596600 chr7:50596586-50596601
7	HDAC2	chr7:50596349-50596798	HepG2	liver:	n/a	chr7:50596708-50596722
8	HEY1	chr7:50596368-50596697	HepG2	liver:	n/a	n/a
9	FOXA1	chr7:50596011-50596736	HepG2	liver:	n/a	n/a
10	HNF4G	chr7:50596231-50596781	HepG2	liver:	n/a	chr7:50596586-50596601 chr7:50596586-50596601 chr7:50596588-50596600 chr7:50596586-50596601 chr7:50596587-50596602
11	HNF4A	chr7:50596335-50596784	HepG2	liver:	n/a	chr7:50596586-50596601 chr7:50596586-50596601 chr7:50596586-50596601 chr7:50596588-50596600 chr7:50596586-50596601
12	MYBL2	chr7:50596244-50596743	HepG2	liver:	n/a	n/a
13	POLR2A	chr7:50596308-50596896	HepG2	liver:	n/a	n/a
14	HNF4G	chr7:50596343-50596785	HepG2	liver:	n/a	chr7:50596586-50596601 chr7:50596586-50596601 chr7:50596588-50596600 chr7:50596586-50596601 chr7:50596587-50596602
15	EP300	chr7:50596020-50596813	HepG2	liver:	n/a	chr7:50596383-50596393
16	HNF4A	chr7:50596315-50596760	HepG2	liver:	n/a	chr7:50596586-50596601 chr7:50596586-50596601 chr7:50596586-50596601 chr7:50596588-50596600 chr7:50596586-50596601

Variant related genes	Relation type
ENSG00000226122	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10239830	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10249420	0.94[CHB][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10265930	0.85[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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10276473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10277662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11575320	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11575463	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11772714	1.00[CEU][hapmap];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	0.84[CHB][hapmap];0.87[ASN][1000 genomes]
rs17733244	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1807066	0.89[EUR][1000 genomes]
rs2044859	0.94[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs2060763	0.89[EUR][1000 genomes]
rs2329371	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2876828	0.90[EUR][1000 genomes]
rs2876829	1.00[CEU][hapmap];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	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735275	0.82[CHB][hapmap]
rs3779074	0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs3779078	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3807552	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3807555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3807556	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3807558	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6950777	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963996	0.92[EUR][1000 genomes]
rs745042	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs745043	1.00[CEU][hapmap];0.82[CHB][hapmap];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	0.88[ASN][1000 genomes]
rs7786398	0.85[JPT][hapmap]
rs7790758	0.92[EUR][1000 genomes]
rs7803440	0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs7803788	0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs7803903	0.88[ASN][1000 genomes]
rs880029	0.90[EUR][1000 genomes]
rs896307	1.00[CEU][hapmap]
rs896309	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][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
rs9942686	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs9942686	FIGNL1	cis	Thyroid	GTEx
rs9942686	FIGNL1	cis	Adipose Subcutaneous	GTEx
rs9942686	FIGNL1	cis	Heart Left Ventricle	GTEx
rs9942686	FIGNL1	cis	lung	GTEx
rs9942686	FIGNL1	cis	Nerve Tibial	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50565200-50609000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr7:50589000-50599200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:50595000-50597200	Enhancers	Liver	Liver
4	chr7:50595200-50597000	Enhancers	Gastric	stomach
5	chr7:50595200-50600000	Enhancers	Pancreas	Pancrea
6	chr7:50595200-50604600	Genic enhancers	Fetal Intestine Small	intestine
7	chr7:50595800-50597000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr7:50595800-50597400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:50595800-50599400	Enhancers	Fetal Intestine Large	intestine
10	chr7:50596000-50596400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:50596000-50596400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr7:50596000-50596800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr7:50596000-50597400	Enhancers	Duodenum Mucosa	Duodenum
14	chr7:50596000-50597800	Enhancers	Stomach Mucosa	stomach
15	chr7:50596200-50596800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:50596200-50597000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr7:50596200-50597000	Flanking Active TSS	HepG2	liver
18	chr7:50596200-50598200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr7:50596200-50598800	Weak transcription	Brain Germinal Matrix	brain
20	chr7:50596200-50599000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:50596200-50599000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr7:50596200-50599200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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