Variant report

Variant	rs13170096
Chromosome Location	chr5:41874935-41874936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SRF	chr5:41874602-41874982	GM12878	blood:	n/a	n/a
2	SRF	chr5:41874513-41875049	ECC-1	luminal epithelium:	n/a	n/a
3	SRF	chr5:41874672-41874939	GM12878	blood:	n/a	n/a
4	SPI1	chr5:41874750-41875012	GM12891	blood:	n/a	n/a
5	SPI1	chr5:41874737-41874995	GM12878	blood:	n/a	n/a
6	SRF	chr5:41874691-41874945	GM12878	blood:	n/a	n/a
7	NFYB	chr5:41874707-41875005	GM12878	blood:	n/a	n/a
8	SRF	chr5:41874588-41874958	HCT-116	colon:	n/a	n/a
9	SRF	chr5:41874656-41875104	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr5:41865564..41868288-chr5:41873378..41876329,4	K562	blood:
2	chr5:41864837..41872825-chr5:41873378..41878557,10	K562	blood:
3	chr5:41872879..41875448-chr5:41895436..41897906,2	K562	blood:
4	chr5:41865404..41878163-chr5:41900217..41908471,28	K562	blood:
5	chr5:41873319..41878163-chr5:41902188..41905939,5	K562	blood:
6	chr5:41874167..41876175-chr5:41878438..41881219,2	MCF-7	breast:
7	chr5:41868991..41872715-chr5:41873991..41877809,9	K562	blood:

No data

Variant related genes	Relation type
OXCT1	TF binding region
ENSG00000248668	Chromatin interaction
ENSG00000205765	Chromatin interaction
ENSG00000083720	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10941559	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11738517	0.84[EUR][1000 genomes]
rs11739106	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11739257	0.91[EUR][1000 genomes]
rs11740524	0.92[EUR][1000 genomes]
rs11740946	0.90[EUR][1000 genomes]
rs11742249	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11744279	0.90[EUR][1000 genomes]
rs11744516	0.90[EUR][1000 genomes]
rs11744623	0.93[EUR][1000 genomes]
rs11746511	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11747881	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11747921	0.90[EUR][1000 genomes]
rs11749008	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11750607	0.99[EUR][1000 genomes]
rs11750760	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11750790	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13153468	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13153837	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13155013	0.85[AMR][1000 genomes]
rs13156367	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13162040	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13163137	0.90[EUR][1000 genomes]
rs13164201	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13165731	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13167578	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13168035	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13169285	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13169977	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13176368	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13177937	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13179852	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13180405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13182336	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13185973	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13189403	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1345781	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1508815	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1508818	0.99[EUR][1000 genomes]
rs16871955	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16871972	0.91[EUR][1000 genomes]
rs16900142	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1876653	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1876654	0.91[EUR][1000 genomes]
rs33967331	0.90[EUR][1000 genomes]
rs34048302	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34071445	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34329864	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34339137	0.90[EUR][1000 genomes]
rs34369972	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34412181	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34500930	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34569700	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34625465	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34663371	0.90[EUR][1000 genomes]
rs34841703	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34873414	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35077044	0.90[EUR][1000 genomes]
rs35244816	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35252930	0.90[EUR][1000 genomes]
rs35343042	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35613904	0.93[EUR][1000 genomes]
rs35748945	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35764180	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35861205	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36005620	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36009913	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36113900	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3926618	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4957430	0.91[EUR][1000 genomes]
rs55817686	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56017638	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60209308	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62360542	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66820325	0.91[EUR][1000 genomes]
rs67114999	0.90[EUR][1000 genomes]
rs67206815	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67715253	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67869805	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6865448	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6866549	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6879341	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6881206	0.94[EUR][1000 genomes]
rs6881873	0.91[EUR][1000 genomes]
rs6883144	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6888816	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6889217	0.90[EUR][1000 genomes]
rs72746918	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72746919	0.89[EUR][1000 genomes]
rs72746957	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7709500	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7712911	0.90[EUR][1000 genomes]
rs7721136	0.88[EUR][1000 genomes]
rs7724934	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7725264	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs951883	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs964267	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9687619	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9763018	0.85[AMR][1000 genomes];0.80[EUR][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	nsv830271	chr5:41716527-41895710	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv2762518	chr5:41780210-41935113	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	108 gene(s)	inside rSNPs	diseases
3	nsv830272	chr5:41833365-41986167	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
4	nsv4811	chr5:41844522-41887353	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv830273	chr5:41867296-42066070	Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13170096	OXCT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41871600-41879200	Weak transcription	Fetal Kidney	kidney
2	chr5:41873000-41875000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:41874600-41875600	Enhancers	GM12878-XiMat	blood
4	chr5:41874800-41875000	Enhancers	Primary T helper cells PMA-I stimulated	--

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