Variant report

Variant	rs3176893
Chromosome Location	chr10:97514617-97514618
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFE2	chr10:97514617-97514646	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCTN3-1	chr10:97512963-97516471	ENSG00000226688.1
2	lnc-TCTN3-1	chr10:97512963-97516471	NONHSAT015766

Variant related genes	Relation type
ENTPD1	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10882622	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs10882623	0.87[EUR][1000 genomes]
rs10882624	0.87[EUR][1000 genomes]
rs10882626	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10882627	0.87[EUR][1000 genomes]
rs10882628	0.87[EUR][1000 genomes]
rs10882629	0.87[EUR][1000 genomes]
rs10882630	0.87[EUR][1000 genomes]
rs10882631	0.87[EUR][1000 genomes]
rs10882632	0.87[EUR][1000 genomes]
rs10882633	0.85[EUR][1000 genomes]
rs10882634	0.87[EUR][1000 genomes]
rs10882635	0.85[EUR][1000 genomes]
rs11188366	0.87[EUR][1000 genomes]
rs11188368	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11188369	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs11188370	0.87[EUR][1000 genomes]
rs11188371	0.87[EUR][1000 genomes]
rs11188376	0.87[EUR][1000 genomes]
rs11541780	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11542152	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12218873	0.87[EUR][1000 genomes]
rs12242866	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12242918	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs12242923	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12248661	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs12250514	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs12255572	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs3176887	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3176892	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3181116	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3181118	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3181125	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3181127	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35168849	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41291572	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62625035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7073436	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7084606	0.87[EUR][1000 genomes]
rs7086374	0.82[EUR][1000 genomes]
rs7097236	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7099430	0.87[EUR][1000 genomes]
rs7099515	0.87[EUR][1000 genomes]
rs7101227	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73325155	0.87[EUR][1000 genomes]
rs73325195	0.87[EUR][1000 genomes]
rs74150947	0.87[EUR][1000 genomes]
rs7896068	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7900437	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7903143	0.85[EUR][1000 genomes]
rs7915682	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7919673	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv895905	chr10:97513362-97686064	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv895906	chr10:97513362-97703650	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3176893	C10orf61	cis	multi-tissue	Pritchard

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97509600-97514800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr10:97513400-97514800	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr10:97514200-97514800	Enhancers	GM12878-XiMat	blood
4	chr10:97514200-97515400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr10:97514400-97515200	Enhancers	Primary B cells from cord blood	blood
6	chr10:97514600-97515400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr10:97514600-97515600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr10:97514600-97516800	Active TSS	Primary hematopoietic stem cells	blood

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