Variant report

Variant	rs6880200
Chromosome Location	chr5:80845428-80845429
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10036712	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10041030	0.85[JPT][hapmap]
rs10042303	0.84[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10075648	0.84[JPT][hapmap]
rs10474031	0.85[JPT][hapmap]
rs10514230	0.85[CEU][hapmap]
rs10942267	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10942269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10942270	0.89[ASN][1000 genomes]
rs11739075	0.84[JPT][hapmap]
rs11740689	0.95[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11740719	0.82[CHB][hapmap]
rs11747277	0.87[ASN][1000 genomes]
rs11949697	0.82[CHB][hapmap]
rs11954000	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs11954508	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12153000	0.92[JPT][hapmap]
rs12515751	0.90[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12521909	0.89[ASN][1000 genomes]
rs13158214	0.85[CEU][hapmap]
rs13182474	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1541830	0.84[JPT][hapmap]
rs2162973	0.84[JPT][hapmap]
rs2972228	0.82[ASN][1000 genomes]
rs2972230	1.00[JPT][hapmap]
rs2972245	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2973341	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs2973343	1.00[JPT][hapmap]
rs2973350	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs35438373	0.86[ASN][1000 genomes]
rs35586490	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3805726	0.82[CHB][hapmap]
rs4274955	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4283765	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4334855	0.89[ASN][1000 genomes]
rs4392600	0.95[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]
rs4426897	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4513668	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]
rs4529168	0.91[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs4599515	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4626317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56005129	0.81[EUR][1000 genomes]
rs62368675	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6452412	0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs6452414	0.84[JPT][hapmap]
rs6452415	0.85[JPT][hapmap]
rs6452416	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs6452419	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66969660	0.86[ASN][1000 genomes]
rs6859225	0.85[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6866155	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6867426	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6868422	0.84[JPT][hapmap];0.80[AMR][1000 genomes]
rs6868748	0.84[JPT][hapmap];0.80[AMR][1000 genomes]
rs6869288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6870325	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6871860	1.00[CEU][hapmap];0.84[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];0.97[ASN][1000 genomes]
rs6874029	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]
rs6874274	0.91[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs6877102	0.84[JPT][hapmap]
rs6878037	0.84[JPT][hapmap]
rs6883488	0.84[JPT][hapmap]
rs6884862	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6887194	0.89[ASN][1000 genomes]
rs6887937	0.84[JPT][hapmap];0.80[AMR][1000 genomes]
rs6890850	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6891181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6895882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6896235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6897189	0.85[JPT][hapmap]
rs7702047	1.00[CEU][hapmap];0.91[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];0.99[ASN][1000 genomes]
rs7707981	0.90[CEU][hapmap]
rs7709916	0.84[CEU][hapmap]
rs7717663	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7719373	0.83[JPT][hapmap]
rs7720123	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7720736	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7721321	0.95[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7725320	0.95[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]
rs7733938	0.81[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7735215	0.87[ASN][1000 genomes]
rs9293275	0.84[JPT][hapmap]
rs9596	0.85[JPT][hapmap]
rs964102	0.82[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.86[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	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

No data

Chromatin state (count:49 , 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	chr5:80821800-80849000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr5:80825200-80865200	Weak transcription	Fetal Brain Male	brain
5	chr5:80827000-80848200	Weak transcription	Left Ventricle	heart
6	chr5:80828800-80863400	Weak transcription	Fetal Lung	lung
7	chr5:80830000-80848800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr5:80830000-80853800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr5:80830200-80848600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr5:80830800-80849600	Weak transcription	Adipose Nuclei	Adipose
11	chr5:80830800-80850000	Weak transcription	Colon Smooth Muscle	Colon
12	chr5:80834000-80849600	Weak transcription	Brain Angular Gyrus	brain
13	chr5:80834000-80851600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:80834400-80867000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr5:80834800-80866400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr5:80834800-80870000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr5:80835000-80852000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr5:80835200-80846400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:80835200-80850400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr5:80835200-80863000	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:80835200-80872800	Weak transcription	Fetal Kidney	kidney
22	chr5:80835200-80875200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr5:80835600-80846800	Strong transcription	Fetal Thymus	thymus
24	chr5:80835600-80876000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr5:80840800-80883400	Weak transcription	HSMM	muscle
26	chr5:80840800-80884600	Weak transcription	Ovary	ovary
27	chr5:80841000-80848600	Weak transcription	HMEC	breast
28	chr5:80841000-80849000	Weak transcription	K562	blood
29	chr5:80841600-80849000	Strong transcription	Dnd41	blood
30	chr5:80841600-80849200	Weak transcription	Brain Anterior Caudate	brain
31	chr5:80842800-80846600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:80843000-80846800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:80843200-80845800	Strong transcription	Thymus	Thymus
34	chr5:80843200-80847200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr5:80843600-80846000	Strong transcription	Primary B cells from cord blood	blood
36	chr5:80843600-80848200	Weak transcription	Fetal Stomach	stomach
37	chr5:80844000-80846000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:80844200-80847200	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr5:80844200-80848800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr5:80844200-80848800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr5:80844200-80884600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:80844600-80847200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:80844600-80849600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr5:80844800-80846200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr5:80844800-80848000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:80845000-80846600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:80845200-80845800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:80845200-80846600	Strong transcription	Primary T cells from cord blood	blood
49	chr5:80845400-80848800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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