Variant report

Variant	rs745042
Chromosome Location	chr7:50544138-50544139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10239830	0.86[EUR][1000 genomes]
rs10267323	0.89[EUR][1000 genomes]
rs10271341	1.00[CEU][hapmap];0.84[JPT][hapmap];0.89[EUR][1000 genomes]
rs10276473	1.00[CEU][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs10277662	0.89[EUR][1000 genomes]
rs11238133	0.83[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs11238134	0.83[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs11575320	1.00[CEU][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes]
rs11575463	1.00[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11761683	0.83[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs11772714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12671474	0.89[EUR][1000 genomes]
rs1376524	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17733244	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1807066	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2060763	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2242042	0.86[EUR][1000 genomes]
rs2329371	1.00[CEU][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs2876828	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2876829	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28889020	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3735273	0.80[CEU][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs3735275	0.83[YRI][hapmap]
rs3779074	0.81[JPT][hapmap]
rs3779078	1.00[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs3807552	0.84[JPT][hapmap]
rs3807555	1.00[CEU][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs3807556	1.00[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs3807558	1.00[CEU][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4449741	0.80[AMR][1000 genomes]
rs6950777	0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs6963996	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs745043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776816	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7790758	0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs880029	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs896307	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs896309	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9942686	1.00[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv606905	chr7:50544063-50565963	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs745042	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs745042	FIGNL1	cis	Heart Left Ventricle	GTEx
rs745042	FIGNL1	cis	Nerve Tibial	GTEx
rs745042	FIGNL1	cis	Adipose Subcutaneous	GTEx
rs745042	FIGNL1	cis	lung	GTEx
rs745042	FIGNL1	cis	Thyroid	GTEx
rs745042	FIGNL1	cis	Artery Tibial	GTEx
rs745042	FIGNL1	cis	multi-tissue	Pritchard

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50535800-50546800	Weak transcription	Pancreas	Pancrea
2	chr7:50535800-50553200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:50536200-50545400	Weak transcription	Right Atrium	heart
4	chr7:50542000-50549600	Weak transcription	Stomach Mucosa	stomach
5	chr7:50542200-50545000	Weak transcription	HepG2	liver
6	chr7:50542200-50546000	Genic enhancers	Fetal Intestine Small	intestine
7	chr7:50542800-50544200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:50542800-50544200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:50543400-50546600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr7:50543600-50595000	Weak transcription	Liver	Liver
11	chr7:50543800-50544200	Genic enhancers	Fetal Intestine Large	intestine
12	chr7:50544000-50544200	Enhancers	Psoas Muscle	Psoas

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