Variant report

Variant	rs11954000
Chromosome Location	chr5:80850092-80850093
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80848254..80852026-chr5:80853882..80857592,4	K562	blood:
2	chr5:80846060..80848703-chr5:80848977..80851148,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10942267	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10942269	0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10942270	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10942275	0.94[CEU][hapmap]
rs11740689	0.92[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11743304	0.83[CEU][hapmap]
rs11747277	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11749863	0.84[CEU][hapmap]
rs11954508	0.97[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12515751	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12521151	0.84[CEU][hapmap]
rs12521909	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13173845	0.83[CEU][hapmap]
rs13182474	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13436668	0.84[CEU][hapmap];0.84[CHB][hapmap];0.80[AMR][1000 genomes]
rs2973341	0.80[JPT][hapmap]
rs35438373	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35586490	0.95[ASN][1000 genomes]
rs4274955	0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4283765	0.86[ASN][1000 genomes]
rs4334855	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4392600	0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4426897	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs4513668	0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4529168	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4599515	0.97[ASN][1000 genomes]
rs4626317	0.86[ASN][1000 genomes]
rs56005129	0.91[AFR][1000 genomes]
rs62368675	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6452419	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs66969660	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6859225	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6866155	0.83[ASN][1000 genomes]
rs6867426	0.88[ASN][1000 genomes]
rs6869288	0.85[ASN][1000 genomes]
rs6871860	0.89[ASN][1000 genomes]
rs6874029	0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs6874274	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6880200	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs6884862	0.81[ASN][1000 genomes]
rs6887194	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6890850	0.88[ASN][1000 genomes]
rs6891181	0.88[ASN][1000 genomes]
rs6895882	0.86[ASN][1000 genomes]
rs6896235	0.86[ASN][1000 genomes]
rs7702047	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7709916	0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs7717663	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7720123	0.85[ASN][1000 genomes]
rs7720445	0.84[CEU][hapmap]
rs7720736	0.81[ASN][1000 genomes]
rs7721321	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7725320	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs7735215	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1028498	chr5:80712364-80860430	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv462221	chr5:80834138-80883110	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv598751	chr5:80834138-80883110	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv525225	chr5:80849084-80883110	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv882233	chr5:80849084-81049187	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80803600-80875200	Weak transcription	Fetal Brain Female	brain
2	chr5:80820200-80851800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:80825200-80865200	Weak transcription	Fetal Brain Male	brain
4	chr5:80828800-80863400	Weak transcription	Fetal Lung	lung
5	chr5:80830000-80853800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr5:80834000-80851600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:80834400-80867000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr5:80834800-80866400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr5:80834800-80870000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr5:80835000-80852000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:80835200-80850400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:80835200-80863000	Weak transcription	Fetal Muscle Leg	muscle
13	chr5:80835200-80872800	Weak transcription	Fetal Kidney	kidney
14	chr5:80835200-80875200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr5:80835600-80876000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr5:80840800-80883400	Weak transcription	HSMM	muscle
17	chr5:80840800-80884600	Weak transcription	Ovary	ovary
18	chr5:80844200-80884600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:80845800-80862000	Weak transcription	Thymus	Thymus
20	chr5:80845800-80863000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:80846200-80850600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr5:80846200-80880600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:80846600-80860000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:80846800-80851800	Weak transcription	Fetal Thymus	thymus
25	chr5:80848000-80856400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:80848600-80850200	Enhancers	Stomach Mucosa	stomach
27	chr5:80848600-80850200	Flanking Active TSS	HUVEC	blood vessel
28	chr5:80848600-80851400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:80848800-80850800	Enhancers	Primary hematopoietic stem cells	blood
30	chr5:80849000-80885600	Weak transcription	Left Ventricle	heart
31	chr5:80849400-80850200	Enhancers	Primary T cells from cord blood	blood
32	chr5:80849400-80856200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:80849600-80850200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:80849600-80850800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr5:80849600-80851400	Enhancers	Dnd41	blood
36	chr5:80849800-80850800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr5:80850000-80850200	Enhancers	Colon Smooth Muscle	Colon
38	chr5:80850000-80860000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr5:80850000-80862000	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links