Variant report

Variant	rs11743952
Chromosome Location	chr5:9140926-9140927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1013720	0.83[CEU][hapmap]
rs1013721	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs11739714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11741669	0.91[CEU][hapmap]
rs11954325	0.86[EUR][1000 genomes]
rs16882062	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16882073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16882076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16882083	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16882086	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16882093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17237642	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17309608	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs253651	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs55784938	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55989322	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58610951	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62342336	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62342337	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6555593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6865778	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6883525	1.00[CEU][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6884247	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7724468	1.00[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv461944	chr5:8758041-9209831	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv597069	chr5:8758041-9209831	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1016937	chr5:8824417-9402871	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv537638	chr5:8824417-9402871	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv918004	chr5:8824417-9402871	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
8	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
9	nsv830200	chr5:9081023-9269495	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv880683	chr5:9091164-9170323	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv881682	chr5:9100211-9151237	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv880323	chr5:9100211-9157454	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv597070	chr5:9100211-9280338	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1020815	chr5:9135207-9425649	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9105200-9145000	Weak transcription	Osteobl	bone
2	chr5:9108800-9147600	Weak transcription	NHDF-Ad	bronchial
3	chr5:9116000-9144600	Weak transcription	Fetal Kidney	kidney
4	chr5:9117600-9144600	Weak transcription	Fetal Lung	lung
5	chr5:9119200-9153200	Weak transcription	Fetal Intestine Large	intestine
6	chr5:9119400-9144600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:9119400-9144600	Weak transcription	Fetal Intestine Small	intestine
8	chr5:9119400-9151800	Weak transcription	Left Ventricle	heart
9	chr5:9119400-9152000	Weak transcription	Right Ventricle	heart
10	chr5:9119400-9152000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:9119600-9144800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr5:9124400-9144600	Weak transcription	Fetal Stomach	stomach
13	chr5:9124600-9144600	Weak transcription	Aorta	Aorta
14	chr5:9127600-9144000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:9132200-9147800	Weak transcription	NHLF	lung
16	chr5:9134000-9152000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:9134400-9156600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:9134800-9144400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:9135200-9144600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:9136600-9144800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:9136800-9144000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:9136800-9144000	Weak transcription	Fetal Muscle Leg	muscle
23	chr5:9136800-9144000	Weak transcription	Lung	lung
24	chr5:9136800-9144000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr5:9136800-9144200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr5:9136800-9144600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr5:9136800-9144600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:9136800-9144600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:9136800-9144600	Weak transcription	Esophagus	oesophagus
30	chr5:9136800-9144800	Weak transcription	Liver	Liver
31	chr5:9136800-9176400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr5:9136800-9189000	Weak transcription	Pancreas	Pancrea
33	chr5:9137000-9144600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:9137000-9144600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:9137000-9151800	Weak transcription	Fetal Heart	heart
36	chr5:9137200-9144800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr5:9137400-9142000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:9139800-9144800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr5:9140400-9142600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:9140600-9141000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr5:9140600-9141600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links