Variant report

Variant	rs3808540
Chromosome Location	chr8:86244170-86244171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1014303	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11261472	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11989660	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1303806	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs1303807	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13259399	0.91[CEU][hapmap];0.85[GIH][hapmap];0.82[EUR][1000 genomes]
rs1390711	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1553015	0.91[CEU][hapmap];0.82[GIH][hapmap];0.86[EUR][1000 genomes]
rs1809820	0.86[EUR][1000 genomes]
rs1995056	0.86[CEU][hapmap];0.82[GIH][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2403104	0.91[CEU][hapmap];0.82[GIH][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3808538	0.82[GIH][hapmap]
rs4150880	0.95[JPT][hapmap]
rs4739700	0.91[CEU][hapmap];0.82[GIH][hapmap];0.84[EUR][1000 genomes]
rs4739702	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4740044	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs4740048	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4740049	0.91[CEU][hapmap];0.82[GIH][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6987641	0.81[EUR][1000 genomes]
rs6993387	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs7008772	0.91[CEU][hapmap]
rs7011926	0.86[CEU][hapmap];0.82[GIH][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7818163	0.91[CEU][hapmap];0.82[GIH][hapmap];0.84[EUR][1000 genomes]
rs7833737	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7837275	0.84[EUR][1000 genomes]
rs903896	0.91[CEU][hapmap];0.82[GIH][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018483	chr8:86142258-86547831	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024759	chr8:86162507-86361533	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv539659	chr8:86162507-86361533	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv971674	chr8:86187966-86338484	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3808540	LRRCC1	cis	Esophagus Mucosa	GTEx
rs3808540	LRRCC1	cis	cerebellum	SCAN
rs3808540	LRRCC1	Cis_1M	lymphoblastoid	RTeQTL
rs3808540	C8orf59	cis	parietal	SCAN
rs3808540	C8orf59	Cis_1M	lymphoblastoid	RTeQTL
rs3808540	C8orf59	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86238800-86254800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr8:86240400-86248600	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links