Variant report

Variant	rs1228868
Chromosome Location	chr7:84030743-84030744
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10236082	0.82[EUR][1000 genomes]
rs10255354	0.86[EUR][1000 genomes]
rs10954752	0.82[EUR][1000 genomes]
rs10954753	0.82[EUR][1000 genomes]
rs11972641	0.82[EUR][1000 genomes]
rs11973476	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1228859	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs1228860	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs1228866	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1228867	0.85[EUR][1000 genomes]
rs1228875	0.85[EUR][1000 genomes]
rs1228876	0.85[EUR][1000 genomes]
rs1228878	0.85[EUR][1000 genomes]
rs1228879	0.87[EUR][1000 genomes]
rs1228880	0.83[EUR][1000 genomes]
rs1228882	0.85[EUR][1000 genomes]
rs1228883	0.85[EUR][1000 genomes]
rs1228939	0.90[CEU][hapmap]
rs1228946	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1228951	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1228952	0.80[EUR][1000 genomes]
rs1228953	0.80[EUR][1000 genomes]
rs1228954	0.80[EUR][1000 genomes]
rs1228956	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1228958	0.80[EUR][1000 genomes]
rs1228959	0.80[EUR][1000 genomes]
rs1228961	0.80[EUR][1000 genomes]
rs1234535	0.82[EUR][1000 genomes]
rs12707647	0.81[EUR][1000 genomes]
rs13227369	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13238916	0.86[EUR][1000 genomes]
rs13437800	0.81[EUR][1000 genomes]
rs13437801	0.82[EUR][1000 genomes]
rs1520102	0.98[ASN][1000 genomes]
rs1557791	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1634605	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1634614	0.80[EUR][1000 genomes]
rs16887703	0.96[ASN][1000 genomes]
rs1715510	0.80[EUR][1000 genomes]
rs1715518	0.98[ASN][1000 genomes]
rs17158998	0.96[ASN][1000 genomes]
rs17159006	1.00[ASN][1000 genomes]
rs17277678	0.82[EUR][1000 genomes]
rs1733998	0.85[EUR][1000 genomes]
rs1733999	0.85[EUR][1000 genomes]
rs1922349	0.90[ASN][1000 genomes]
rs1974512	0.86[EUR][1000 genomes]
rs1987325	0.86[EUR][1000 genomes]
rs2106965	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2158169	0.86[EUR][1000 genomes]
rs2189119	0.82[EUR][1000 genomes]
rs2214362	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2214749	0.98[ASN][1000 genomes]
rs2372453	0.86[EUR][1000 genomes]
rs2372454	0.80[EUR][1000 genomes]
rs2428807	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2522371	0.86[EUR][1000 genomes]
rs2527522	0.86[ASN][1000 genomes]
rs2527527	0.88[ASN][1000 genomes]
rs2527529	0.88[ASN][1000 genomes]
rs2527530	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2527532	0.87[ASN][1000 genomes]
rs2527533	0.88[ASN][1000 genomes]
rs2527535	0.88[ASN][1000 genomes]
rs2527536	0.85[ASN][1000 genomes]
rs2527537	0.88[ASN][1000 genomes]
rs2527538	0.88[ASN][1000 genomes]
rs2681435	0.85[EUR][1000 genomes]
rs2706903	0.88[ASN][1000 genomes]
rs2706912	0.98[ASN][1000 genomes]
rs2706913	0.98[ASN][1000 genomes]
rs2706916	0.96[ASN][1000 genomes]
rs2715032	0.88[ASN][1000 genomes]
rs2715037	0.87[ASN][1000 genomes]
rs2715044	0.90[ASN][1000 genomes]
rs2715045	0.90[ASN][1000 genomes]
rs2715046	0.90[ASN][1000 genomes]
rs2715047	0.90[ASN][1000 genomes]
rs2888321	0.86[EUR][1000 genomes]
rs2888322	1.00[ASN][1000 genomes]
rs4016106	0.85[ASN][1000 genomes]
rs4728554	0.86[EUR][1000 genomes]
rs4732548	0.82[EUR][1000 genomes]
rs4732549	0.86[EUR][1000 genomes]
rs505758	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs519663	0.86[EUR][1000 genomes]
rs520178	0.99[ASN][1000 genomes]
rs521595	0.86[EUR][1000 genomes]
rs524163	0.83[EUR][1000 genomes]
rs524301	0.86[EUR][1000 genomes]
rs526991	0.98[ASN][1000 genomes]
rs529539	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs530698	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531582	1.00[ASN][1000 genomes]
rs538712	0.85[EUR][1000 genomes]
rs539643	0.86[EUR][1000 genomes]
rs540454	0.86[EUR][1000 genomes]
rs549975	0.86[EUR][1000 genomes]
rs555632	0.94[ASN][1000 genomes]
rs559041	1.00[ASN][1000 genomes]
rs560627	0.82[EUR][1000 genomes]
rs56144625	1.00[ASN][1000 genomes]
rs561955	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568973	0.86[EUR][1000 genomes]
rs577142	0.91[EUR][1000 genomes]
rs607120	0.86[EUR][1000 genomes]
rs608459	0.86[EUR][1000 genomes]
rs609308	0.86[EUR][1000 genomes]
rs611442	0.86[EUR][1000 genomes]
rs611503	0.86[EUR][1000 genomes]
rs612337	0.82[EUR][1000 genomes]
rs612856	0.86[EUR][1000 genomes]
rs613335	0.86[EUR][1000 genomes]
rs620892	0.85[EUR][1000 genomes]
rs621903	0.86[EUR][1000 genomes]
rs622514	0.85[AFR][1000 genomes]
rs623289	0.86[EUR][1000 genomes]
rs62474863	0.85[EUR][1000 genomes]
rs625480	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633234	0.85[EUR][1000 genomes]
rs642572	0.82[EUR][1000 genomes]
rs648653	0.82[EUR][1000 genomes]
rs73711542	0.95[ASN][1000 genomes]
rs73711549	0.99[ASN][1000 genomes]
rs7783073	0.96[ASN][1000 genomes]
rs7789787	0.86[EUR][1000 genomes]
rs7808081	0.86[EUR][1000 genomes]
rs916865	0.85[EUR][1000 genomes]
rs961201	0.86[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	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
4	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
5	nsv534431	chr7:84001059-84138511	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv949446	chr7:84003501-84763823	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1228868	SEMA3C	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:84029800-84032200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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