Variant report

Variant	rs1382228
Chromosome Location	chr15:54155564-54155565
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1382233	0.89[ASN][1000 genomes]
rs1478194	0.91[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1478196	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1478197	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1478198	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1478206	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1947761	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1947762	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2246052	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2255994	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256003	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414261	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2616922	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2616935	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2711641	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2725602	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2725603	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2725611	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4294761	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4465558	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4776181	0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7172643	1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904223	chr15:53665247-54340070	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv904224	chr15:53668018-54210677	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1052235	chr15:53677524-54618723	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv542388	chr15:53677524-54618723	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv904226	chr15:53883244-54458310	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv457144	chr15:53890362-54455757	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv569440	chr15:53890362-54455757	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv569441	chr15:53890362-54456754	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv457145	chr15:53890393-54456754	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv569442	chr15:53890393-54456754	Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv949528	chr15:54041154-54281981	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv457147	chr15:54080810-54156980	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv569452	chr15:54080810-54156980	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv817539	chr15:54132584-55095235	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
15	nsv457148	chr15:54153462-54172552	Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv569453	chr15:54153462-54172552	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1382228	IGSF11	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54153800-54156200	Enhancers	Fetal Intestine Large	intestine
2	chr15:54153800-54156200	Enhancers	Fetal Intestine Small	intestine
3	chr15:54154400-54167800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:54154600-54155600	Enhancers	Fetal Kidney	kidney
5	chr15:54154800-54155600	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr15:54155400-54155600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:54155400-54155600	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links