Variant report

Variant	rs7700373
Chromosome Location	chr5:118180935-118180936
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10434765	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs12186800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1355377	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1533107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17144678	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17372823	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4895184	0.93[CEU][hapmap];0.83[TSI][hapmap]
rs4895356	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs607412	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs612000	0.82[ASN][1000 genomes]
rs612719	0.82[ASN][1000 genomes]
rs7712081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882767	chr5:117931730-118385691	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv599562	chr5:118122504-118230640	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv882771	chr5:118170135-118230640	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv882772	chr5:118173127-118230640	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv882773	chr5:118175640-118241854	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7700373	SEMA6A	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118167800-118186400	Weak transcription	Liver	Liver
2	chr5:118169600-118208600	Weak transcription	Aorta	Aorta
3	chr5:118172200-118188600	Weak transcription	Primary T cells from cord blood	blood
4	chr5:118175400-118186200	Weak transcription	Primary B cells from cord blood	blood
5	chr5:118179400-118182000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr5:118180800-118181800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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