Variant report

Variant	rs17277678
Chromosome Location	chr7:83964829-83964830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10236082	0.90[EUR][1000 genomes]
rs10255354	0.87[EUR][1000 genomes]
rs10954752	0.90[EUR][1000 genomes]
rs10954753	0.90[EUR][1000 genomes]
rs11972641	0.90[EUR][1000 genomes]
rs11973476	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1228859	0.90[CEU][hapmap]
rs1228860	0.91[CEU][hapmap]
rs1228866	0.81[EUR][1000 genomes]
rs1228868	0.82[EUR][1000 genomes]
rs1228939	0.90[CEU][hapmap]
rs12707647	0.89[EUR][1000 genomes]
rs13227369	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13238916	0.88[EUR][1000 genomes]
rs13437800	0.88[EUR][1000 genomes]
rs13437801	0.90[EUR][1000 genomes]
rs1557791	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1974512	0.88[EUR][1000 genomes]
rs1987325	0.88[EUR][1000 genomes]
rs2106965	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2158169	0.86[EUR][1000 genomes]
rs2189119	0.90[EUR][1000 genomes]
rs2189121	0.86[ASN][1000 genomes]
rs2214362	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2372453	0.86[EUR][1000 genomes]
rs2372454	0.80[EUR][1000 genomes]
rs2522371	0.87[EUR][1000 genomes]
rs2681435	0.86[EUR][1000 genomes]
rs2888321	0.86[EUR][1000 genomes]
rs4728554	0.88[EUR][1000 genomes]
rs4732548	0.90[EUR][1000 genomes]
rs4732549	0.88[EUR][1000 genomes]
rs505758	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs519663	0.88[EUR][1000 genomes]
rs521595	0.87[EUR][1000 genomes]
rs524163	0.84[EUR][1000 genomes]
rs524301	0.87[EUR][1000 genomes]
rs529539	0.87[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap]
rs530698	0.81[EUR][1000 genomes]
rs538712	0.89[EUR][1000 genomes]
rs539643	0.88[EUR][1000 genomes]
rs540454	0.88[EUR][1000 genomes]
rs549975	0.88[EUR][1000 genomes]
rs560627	0.90[EUR][1000 genomes]
rs561955	0.80[EUR][1000 genomes]
rs568973	0.88[EUR][1000 genomes]
rs577142	0.83[EUR][1000 genomes]
rs607120	0.88[EUR][1000 genomes]
rs608459	0.88[EUR][1000 genomes]
rs609308	0.88[EUR][1000 genomes]
rs611442	0.88[EUR][1000 genomes]
rs611503	0.88[EUR][1000 genomes]
rs612337	0.90[EUR][1000 genomes]
rs612856	0.88[EUR][1000 genomes]
rs613335	0.88[EUR][1000 genomes]
rs620892	0.86[EUR][1000 genomes]
rs621903	0.88[EUR][1000 genomes]
rs623289	0.87[EUR][1000 genomes]
rs625480	0.81[EUR][1000 genomes]
rs633234	0.86[EUR][1000 genomes]
rs642572	0.90[EUR][1000 genomes]
rs648653	0.90[EUR][1000 genomes]
rs650395	0.88[EUR][1000 genomes]
rs7789787	0.88[EUR][1000 genomes]
rs7808081	0.88[EUR][1000 genomes]
rs961201	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1017884	chr7:83724138-83972995	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv538995	chr7:83724138-83972995	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	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
5	esv1793815	chr7:83909503-83997755	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	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
7	nsv888632	chr7:83958436-83993099	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases
8	esv3394848	chr7:83962716-83966614	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17277678	SEMA3C	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83947200-83966800	Weak transcription	NHDF-Ad	bronchial
2	chr7:83961200-83965800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:83961400-83965000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr7:83961400-83965200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:83961400-83965400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:83961400-83965800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr7:83964200-83966600	Weak transcription	Brain Germinal Matrix	brain

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