Variant report

Variant	rs1557791
Chromosome Location	chr7:83996194-83996195
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10236082	0.90[EUR][1000 genomes]
rs10255354	0.94[EUR][1000 genomes]
rs10954752	0.90[EUR][1000 genomes]
rs10954753	0.90[EUR][1000 genomes]
rs11972641	0.90[EUR][1000 genomes]
rs11973476	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1228859	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs1228860	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs1228866	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1228867	0.85[EUR][1000 genomes]
rs1228868	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1228875	0.85[EUR][1000 genomes]
rs1228876	0.85[EUR][1000 genomes]
rs1228878	0.85[EUR][1000 genomes]
rs1228879	0.83[EUR][1000 genomes]
rs1228880	0.82[EUR][1000 genomes]
rs1228882	0.84[EUR][1000 genomes]
rs1228883	0.84[EUR][1000 genomes]
rs1228939	0.85[CEU][hapmap]
rs1228951	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1228956	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1234535	0.88[EUR][1000 genomes]
rs12707647	0.88[EUR][1000 genomes]
rs13227369	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238916	0.94[EUR][1000 genomes]
rs13437800	0.88[EUR][1000 genomes]
rs13437801	0.90[EUR][1000 genomes]
rs1520102	0.83[ASN][1000 genomes]
rs1634605	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16887703	0.89[ASN][1000 genomes]
rs1715518	0.83[ASN][1000 genomes]
rs17158998	0.85[ASN][1000 genomes]
rs17159006	0.85[ASN][1000 genomes]
rs17277678	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1733998	0.86[EUR][1000 genomes]
rs1733999	0.86[EUR][1000 genomes]
rs1974512	0.94[EUR][1000 genomes]
rs1987325	0.94[EUR][1000 genomes]
rs2106965	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2158169	0.95[EUR][1000 genomes]
rs2189119	0.90[EUR][1000 genomes]
rs2214362	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214749	0.83[ASN][1000 genomes]
rs2372453	0.95[EUR][1000 genomes]
rs2372454	0.90[EUR][1000 genomes]
rs2428807	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2522371	0.93[EUR][1000 genomes]
rs2681435	0.92[EUR][1000 genomes]
rs2706912	0.83[ASN][1000 genomes]
rs2706913	0.83[ASN][1000 genomes]
rs2706916	0.89[ASN][1000 genomes]
rs2888321	0.95[EUR][1000 genomes]
rs2888322	0.85[ASN][1000 genomes]
rs4728554	0.94[EUR][1000 genomes]
rs4732548	0.90[EUR][1000 genomes]
rs4732549	0.94[EUR][1000 genomes]
rs505758	0.81[CEU][hapmap];0.93[EUR][1000 genomes]
rs519663	0.94[EUR][1000 genomes]
rs520178	0.86[ASN][1000 genomes]
rs521595	0.93[EUR][1000 genomes]
rs524163	0.90[EUR][1000 genomes]
rs524301	0.93[EUR][1000 genomes]
rs526991	0.87[ASN][1000 genomes]
rs529539	0.81[CHB][hapmap];0.89[ASN][1000 genomes]
rs530698	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs531582	0.85[ASN][1000 genomes]
rs538712	0.92[EUR][1000 genomes]
rs539643	0.94[EUR][1000 genomes]
rs540454	0.94[EUR][1000 genomes]
rs549975	0.94[EUR][1000 genomes]
rs555632	0.87[ASN][1000 genomes]
rs559041	0.85[ASN][1000 genomes]
rs560627	0.90[EUR][1000 genomes]
rs56144625	0.85[ASN][1000 genomes]
rs561955	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs568973	0.94[EUR][1000 genomes]
rs577142	0.93[EUR][1000 genomes]
rs607120	0.94[EUR][1000 genomes]
rs608459	0.94[EUR][1000 genomes]
rs609308	0.94[EUR][1000 genomes]
rs611442	0.94[EUR][1000 genomes]
rs611503	0.94[EUR][1000 genomes]
rs612337	0.90[EUR][1000 genomes]
rs612856	0.94[EUR][1000 genomes]
rs613335	0.94[EUR][1000 genomes]
rs620892	0.92[EUR][1000 genomes]
rs621903	0.94[EUR][1000 genomes]
rs623289	0.93[EUR][1000 genomes]
rs62472601	0.81[EUR][1000 genomes]
rs62474863	0.85[EUR][1000 genomes]
rs625480	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs633234	0.92[EUR][1000 genomes]
rs642572	0.90[EUR][1000 genomes]
rs648653	0.90[EUR][1000 genomes]
rs650395	0.87[EUR][1000 genomes]
rs73711542	0.88[ASN][1000 genomes]
rs73711549	0.86[ASN][1000 genomes]
rs7783073	0.89[ASN][1000 genomes]
rs7789787	0.94[EUR][1000 genomes]
rs7808081	0.94[EUR][1000 genomes]
rs916865	0.85[EUR][1000 genomes]
rs961201	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529344	chr7:83714286-84592857	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	esv2754468	chr7:83851249-84166749	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv1793815	chr7:83909503-83997755	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv888631	chr7:83911271-84010005	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1023848	chr7:83985028-84101774	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2761342	chr7:83985028-84101798	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1557791	SEMA3C	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83994400-83999400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr7:83994600-84001200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr7:83994800-84001200	Weak transcription	NHDF-Ad	bronchial
4	chr7:83996000-83996400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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