Variant report

Variant	rs11956440
Chromosome Location	chr5:106762175-106762176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10085055	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11242636	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13178242	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13182976	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1975009	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28683545	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34366978	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34583348	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35021422	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3756544	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs3776792	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3797510	1.00[CEU][hapmap];0.86[CHD][hapmap];0.82[MEX][hapmap]
rs3797513	1.00[CEU][hapmap];0.89[CHD][hapmap];0.82[MEX][hapmap]
rs3797516	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes]
rs3797517	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3797521	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3797527	0.88[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3822565	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3873122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3873123	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3901010	0.88[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs58696640	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66505151	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6868410	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72785829	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7703776	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers 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	6 gene(s)	inside rSNPs	diseases
2	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106739600-106762600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:106751600-106764400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:106751800-106765800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr5:106751800-106767800	Weak transcription	Stomach Mucosa	stomach
5	chr5:106753400-106764400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:106754000-106767600	Weak transcription	Fetal Stomach	stomach
7	chr5:106754200-106763800	Weak transcription	GM12878-XiMat	blood
8	chr5:106754800-106762200	Weak transcription	Fetal Lung	lung
9	chr5:106756400-106768200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr5:106756600-106772000	Weak transcription	Esophagus	oesophagus
11	chr5:106758200-106762400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:106758600-106763800	Weak transcription	Fetal Heart	heart
13	chr5:106758600-106765800	Weak transcription	Aorta	Aorta
14	chr5:106758600-106765800	Weak transcription	Fetal Kidney	kidney
15	chr5:106758600-106767800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr5:106758600-106767800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:106758600-106767800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:106758600-106767800	Weak transcription	Left Ventricle	heart
19	chr5:106758600-106771200	Weak transcription	Right Ventricle	heart
20	chr5:106758600-106772000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:106758600-106785000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr5:106759000-106762600	Enhancers	Muscle Satellite Cultured Cells	--
23	chr5:106759000-106762600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:106759200-106762800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:106759400-106762200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:106759400-106762200	Enhancers	NH-A	brain
27	chr5:106759400-106762400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:106759400-106762400	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr5:106759400-106762400	Enhancers	Osteobl	bone
30	chr5:106759400-106764200	Enhancers	HSMM	muscle
31	chr5:106759600-106762200	Enhancers	Placenta Amnion	Placenta Amnion
32	chr5:106759600-106767600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr5:106760200-106762200	Flanking Active TSS	A549	lung
34	chr5:106760200-106762200	Enhancers	HSMMtube	muscle
35	chr5:106760200-106762400	Enhancers	NHLF	lung
36	chr5:106760400-106762200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:106760400-106763200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:106760400-106764600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:106760600-106762200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:106761000-106762200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:106761600-106762200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:106761600-106762200	Enhancers	Rectal Smooth Muscle	rectum
43	chr5:106761600-106762600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:106761600-106762600	Enhancers	NHEK	skin
45	chr5:106761600-106763200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:106761600-106763200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr5:106761600-106763200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:106761600-106766200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:106761800-106762400	Enhancers	NHDF-Ad	bronchial
50	chr5:106761800-106763200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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