Variant report

Variant	rs17516389
Chromosome Location	chr4:119239267-119239268
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10017003	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11931079	1.00[ASN][1000 genomes]
rs13101451	1.00[ASN][1000 genomes]
rs13103629	1.00[ASN][1000 genomes]
rs13104251	1.00[ASN][1000 genomes]
rs13109564	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13119795	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13120016	1.00[ASN][1000 genomes]
rs13123277	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13125461	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13127368	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13128545	1.00[ASN][1000 genomes]
rs13130953	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13131623	1.00[ASN][1000 genomes]
rs13132957	0.81[CEU][hapmap];1.00[ASN][1000 genomes]
rs13135360	0.89[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13136897	1.00[ASN][1000 genomes]
rs13138385	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs13138982	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13140433	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13141841	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13142184	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13144171	1.00[ASN][1000 genomes]
rs13144419	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13146959	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13151098	1.00[ASN][1000 genomes]
rs1608506	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17516164	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17516219	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17516233	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17516512	0.81[CEU][hapmap];1.00[ASN][1000 genomes]
rs17516526	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs17594018	1.00[ASN][1000 genomes]
rs17594257	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17594447	1.00[ASN][1000 genomes]
rs17594468	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17594559	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17594740	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17594782	0.81[CEU][hapmap];1.00[ASN][1000 genomes]
rs17626479	1.00[ASN][1000 genomes]
rs34082100	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34101813	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34185290	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34202571	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34284204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34302716	1.00[ASN][1000 genomes]
rs34531766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34723948	1.00[ASN][1000 genomes]
rs34804902	1.00[ASN][1000 genomes]
rs34835262	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34928611	1.00[ASN][1000 genomes]
rs34958556	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35054481	1.00[ASN][1000 genomes]
rs35215908	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35420005	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35553303	1.00[ASN][1000 genomes]
rs35612621	1.00[ASN][1000 genomes]
rs35650624	1.00[ASN][1000 genomes]
rs35749089	1.00[ASN][1000 genomes]
rs35774897	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35861609	1.00[ASN][1000 genomes]
rs35872631	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35875491	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35876590	1.00[ASN][1000 genomes]
rs35909687	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35983699	1.00[ASN][1000 genomes]
rs36058627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55699931	1.00[ASN][1000 genomes]
rs71608346	1.00[ASN][1000 genomes]
rs71608350	1.00[ASN][1000 genomes]
rs71608351	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71608352	1.00[ASN][1000 genomes]
rs71608355	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71608356	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71608358	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71608359	1.00[ASN][1000 genomes]
rs71608361	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71608363	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1009076	chr4:118949490-119269424	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1001236	chr4:118949490-119271243	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv34038	chr4:119035124-119455391	Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1001138	chr4:119095147-119461837	Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv537230	chr4:119095147-119461837	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1002771	chr4:119125361-119571237	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1003731	chr4:119138262-119506032	Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv10558	chr4:119234576-119243935	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119202800-119267200	Weak transcription	Stomach Mucosa	stomach
2	chr4:119209600-119258600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:119210000-119259200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:119210200-119258600	Weak transcription	HMEC	breast
5	chr4:119212600-119259200	Weak transcription	NHEK	skin
6	chr4:119213000-119240600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr4:119216400-119249800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:119216600-119244000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:119217400-119243400	Weak transcription	Fetal Lung	lung
10	chr4:119220200-119240200	Weak transcription	Osteobl	bone
11	chr4:119220200-119260000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:119229000-119267200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:119233000-119246600	Weak transcription	Fetal Stomach	stomach
14	chr4:119234600-119239400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:119234600-119243800	Weak transcription	NHDF-Ad	bronchial
16	chr4:119234800-119239400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:119234800-119239400	Weak transcription	Fetal Brain Male	brain
18	chr4:119237600-119250800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:119239000-119240600	Strong transcription	NHLF	lung
20	chr4:119239000-119242200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links