Variant report

Variant	rs11883422
Chromosome Location	chr19:39537089-39537090
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39521423..39523663-chr19:39535001..39537936,2	MCF-7	breast:
2	chr19:39536592..39538414-chr19:39541757..39543284,2	MCF-7	breast:
3	chr19:39528736..39531074-chr19:39534796..39537090,2	K562	blood:
4	chr19:39521025..39525658-chr19:39535006..39538345,5	MCF-7	breast:
5	chr19:39522295..39523922-chr19:39537003..39539265,2	K562	blood:

Variant related genes	Relation type
ENSG00000161243	Chromatin interaction
ENSG00000267992	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10406222	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10416823	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10424632	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10424827	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10426645	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10426661	0.90[ASN][1000 genomes]
rs1062261	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10853723	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10853724	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083499	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11083500	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11083501	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083502	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1139251	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11667641	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11670486	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11670520	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11673044	0.80[ASN][1000 genomes]
rs11673637	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11880441	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12609806	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12610200	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12610248	0.83[ASN][1000 genomes]
rs12971842	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12972850	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12972978	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12978163	0.88[ASN][1000 genomes]
rs12978749	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12982199	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12982349	0.90[ASN][1000 genomes]
rs12982529	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12985447	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1651748	0.87[EUR][1000 genomes]
rs1840745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1840746	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1840747	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1840748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1864191	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1869983	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36154890	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3848623	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4280369	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802007	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4802009	0.85[ASN][1000 genomes]
rs4803181	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803185	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803186	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803187	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803188	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58897626	0.91[ASN][1000 genomes]
rs60775146	0.91[ASN][1000 genomes]
rs62119538	0.91[ASN][1000 genomes]
rs628335	0.89[ASN][1000 genomes]
rs650027	0.81[CEU][hapmap]
rs6508835	0.87[ASN][1000 genomes]
rs6508836	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6508837	0.87[ASN][1000 genomes]
rs6508838	0.90[ASN][1000 genomes]
rs6508839	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6508840	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6508841	0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs6508842	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6508843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs681496	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7247801	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7248513	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7248652	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7250110	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7250431	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251264	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7255211	0.91[ASN][1000 genomes]
rs7256126	0.89[ASN][1000 genomes]
rs7258862	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7259064	0.90[ASN][1000 genomes]
rs7259197	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs7259801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8100503	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8103187	0.86[ASN][1000 genomes]
rs8104751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8104899	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8104990	0.81[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8105865	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109176	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963126	chr19:39521120-39552490	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2760517	chr19:39530012-39544234	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv526711	chr19:39533754-39538592	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv458570	chr19:39533754-39538592	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv579507	chr19:39533754-39538592	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11883422	FBXO27	cis	Esophagus Mucosa	GTEx
rs11883422	CTB-189B5.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11883422	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx
rs11883422	CTB-189B5.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39530800-39543000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr19:39535400-39538800	Enhancers	Fetal Intestine Large	intestine
3	chr19:39535400-39538800	Enhancers	Fetal Intestine Small	intestine
4	chr19:39535800-39538800	Enhancers	Duodenum Mucosa	Duodenum
5	chr19:39536400-39537200	Enhancers	Placenta	Placenta
6	chr19:39536400-39537200	Enhancers	Hela-S3	cervix
7	chr19:39536400-39537400	Flanking Active TSS	K562	blood
8	chr19:39536400-39538200	Enhancers	Stomach Mucosa	stomach
9	chr19:39536600-39537400	Enhancers	GM12878-XiMat	blood
10	chr19:39536600-39537600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:39536800-39537200	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr19:39536800-39537400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
13	chr19:39537000-39537200	Enhancers	HepG2	liver
14	chr19:39537000-39537600	Enhancers	A549	lung

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