Variant report

Variant	rs6869839
Chromosome Location	chr5:80869892-80869893
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10036942	1.00[ASN][1000 genomes]
rs10050981	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10054360	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10056236	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10057707	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10060208	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10060828	0.89[ASN][1000 genomes]
rs10064862	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10066110	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10069094	0.86[AFR][1000 genomes]
rs10473849	0.89[ASN][1000 genomes]
rs10474032	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10474033	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10474035	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514221	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942268	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13354281	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13357855	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs16876417	0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs16898989	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28465130	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs28546170	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56414093	0.89[ASN][1000 genomes]
rs57587453	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57681369	0.89[ASN][1000 genomes]
rs58238009	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58652756	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61561045	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452417	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872668	0.89[ASN][1000 genomes]
rs6884379	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6887061	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6888401	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6893886	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6896772	0.89[ASN][1000 genomes]
rs6897373	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898968	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133677	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73133692	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73135608	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135614	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73135635	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73766239	0.89[ASN][1000 genomes]
rs7717767	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9293277	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9641	0.89[ASN][1000 genomes]
rs9986216	0.86[AFR][1000 genomes];1.00[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	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
2	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
3	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
4	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
5	esv2763467	chr5:80852616-80872981	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv882234	chr5:80853708-80966666	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80803600-80875200	Weak transcription	Fetal Brain Female	brain
2	chr5:80834800-80870000	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr5:80835200-80872800	Weak transcription	Fetal Kidney	kidney
4	chr5:80835200-80875200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr5:80835600-80876000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr5:80840800-80883400	Weak transcription	HSMM	muscle
7	chr5:80840800-80884600	Weak transcription	Ovary	ovary
8	chr5:80844200-80884600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:80846200-80880600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:80849000-80885600	Weak transcription	Left Ventricle	heart
11	chr5:80860200-80878800	Weak transcription	Esophagus	oesophagus
12	chr5:80862400-80874800	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:80862800-80878800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr5:80863800-80872000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:80864200-80870400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr5:80864200-80886400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:80864200-80894200	Weak transcription	Fetal Lung	lung
18	chr5:80864600-80894200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr5:80864800-80875200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:80865000-80871600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:80865000-80875200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:80867200-80870400	Weak transcription	Colon Smooth Muscle	Colon
23	chr5:80867800-80870600	Strong transcription	Fetal Thymus	thymus
24	chr5:80867800-80875200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr5:80868200-80871200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:80868600-80875200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:80868800-80871000	Weak transcription	HUVEC	blood vessel
28	chr5:80869200-80875400	Weak transcription	Primary T cells from cord blood	blood
29	chr5:80869400-80870000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr5:80869400-80870400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:80869400-80871800	Strong transcription	Dnd41	blood
32	chr5:80869400-80887600	Weak transcription	Fetal Stomach	stomach
33	chr5:80869600-80870200	Strong transcription	GM12878-XiMat	blood
34	chr5:80869800-80870000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr5:80869800-80870800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:80869800-80870800	ZNF genes & repeats	Primary B cells from cord blood	blood
37	chr5:80869800-80886400	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links