Variant report

Variant	rs6888401
Chromosome Location	chr5:80864809-80864810
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10036942	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10050981	0.90[ASN][1000 genomes]
rs10054360	1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[ASN][1000 genomes]
rs10056236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10057707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10060208	1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10064862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10066110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10069094	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs10474032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474035	1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[ASN][1000 genomes]
rs10514221	1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10942268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12515751	0.95[YRI][hapmap]
rs13354281	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13357855	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16876417	1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs16898989	1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs28465130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28546170	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4529168	0.90[YRI][hapmap]
rs57587453	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs58238009	0.83[AFR][1000 genomes]
rs58652756	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs61561045	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6452417	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6859225	0.90[YRI][hapmap]
rs6869839	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6884379	0.90[ASN][1000 genomes]
rs6887061	1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6893886	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6896772	1.00[JPT][hapmap]
rs6897373	1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[ASN][1000 genomes]
rs6898968	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73133677	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73133692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135608	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73135614	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135635	0.85[AFR][1000 genomes]
rs7717767	1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7721321	1.00[YRI][hapmap]
rs9293277	1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9641	1.00[JPT][hapmap]
rs9986216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv965529	chr5:80864599-80867893	Strong transcription Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80803600-80875200	Weak transcription	Fetal Brain Female	brain
2	chr5:80825200-80865200	Weak transcription	Fetal Brain Male	brain
3	chr5:80834400-80867000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:80834800-80866400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr5:80834800-80870000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr5:80835200-80872800	Weak transcription	Fetal Kidney	kidney
7	chr5:80835200-80875200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr5:80835600-80876000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr5:80840800-80883400	Weak transcription	HSMM	muscle
10	chr5:80840800-80884600	Weak transcription	Ovary	ovary
11	chr5:80844200-80884600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:80846200-80880600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:80849000-80885600	Weak transcription	Left Ventricle	heart
14	chr5:80850800-80866800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr5:80860200-80878800	Weak transcription	Esophagus	oesophagus
16	chr5:80860400-80866800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr5:80861600-80867200	Strong transcription	Dnd41	blood
18	chr5:80862000-80865000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
19	chr5:80862000-80865400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:80862400-80865600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr5:80862400-80874800	Weak transcription	Brain Hippocampus Middle	brain
22	chr5:80862800-80878800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:80863000-80865600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:80863400-80865200	Strong transcription	Fetal Thymus	thymus
25	chr5:80863800-80865200	Weak transcription	Fetal Muscle Leg	muscle
26	chr5:80863800-80866000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr5:80863800-80867200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:80863800-80868800	Weak transcription	Fetal Stomach	stomach
29	chr5:80863800-80872000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr5:80864200-80870400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr5:80864200-80886400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:80864200-80894200	Weak transcription	Fetal Lung	lung
33	chr5:80864400-80868200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr5:80864400-80868200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:80864400-80868600	Weak transcription	Primary T cells from cord blood	blood
36	chr5:80864600-80865000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:80864600-80866200	Weak transcription	Primary B cells from cord blood	blood
38	chr5:80864600-80866800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr5:80864600-80867400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr5:80864600-80894200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr5:80864800-80865200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:80864800-80868200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:80864800-80869000	Weak transcription	Thymus	Thymus
44	chr5:80864800-80875200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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