Variant report

Variant	rs6452415
Chromosome Location	chr5:80776834-80776835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80768944..80770618-chr5:80775514..80777278,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10035291	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10036712	0.83[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10041030	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10042201	0.82[CHB][hapmap]
rs10042303	0.81[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs10043164	0.81[ASN][1000 genomes]
rs10056711	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068144	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10075648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942266	0.94[ASN][1000 genomes]
rs11739075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740719	0.92[CHB][hapmap]
rs11742106	0.80[CEU][hapmap]
rs11949697	0.92[CHB][hapmap]
rs12153000	0.93[JPT][hapmap]
rs12697705	0.87[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13159500	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13171682	0.98[ASN][1000 genomes]
rs1541830	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2162973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396170	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34150522	0.81[ASN][1000 genomes]
rs34699788	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35224297	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805726	0.92[CHB][hapmap]
rs6452407	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6452410	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452411	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs6452412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452414	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6452416	1.00[JPT][hapmap]
rs6865796	0.90[CEU][hapmap]
rs6866156	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866727	0.91[CEU][hapmap]
rs6866741	0.84[ASN][1000 genomes]
rs6868422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6868748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872793	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6874237	0.86[ASN][1000 genomes]
rs6877102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878037	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6880200	0.85[JPT][hapmap]
rs6883488	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6887937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6897189	0.91[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7702374	0.91[CEU][hapmap]
rs7711020	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719373	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725126	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7733938	0.83[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs7737895	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs9293275	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9596	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs964102	0.82[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs9918175	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80703200-80779200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:80735400-80778600	Weak transcription	Aorta	Aorta
3	chr5:80766200-80800000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:80769800-80778600	Weak transcription	K562	blood
5	chr5:80769800-80779600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:80770000-80777600	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:80770000-80778000	Weak transcription	Thymus	Thymus
8	chr5:80770000-80778200	Weak transcription	Primary B cells from cord blood	blood
9	chr5:80770000-80779400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr5:80770000-80781000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr5:80770000-80782600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:80770000-80787800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:80770000-80789000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:80770000-80790400	Weak transcription	Right Ventricle	heart
15	chr5:80770000-80797800	Weak transcription	GM12878-XiMat	blood
16	chr5:80770000-80800200	Weak transcription	Brain Anterior Caudate	brain
17	chr5:80770000-80801600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:80770000-80801600	Weak transcription	NHLF	lung
19	chr5:80770000-80803000	Weak transcription	Fetal Kidney	kidney
20	chr5:80770000-80811000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr5:80770000-80812000	Weak transcription	Left Ventricle	heart
22	chr5:80770200-80782600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:80770200-80782600	Weak transcription	Adipose Nuclei	Adipose
24	chr5:80770200-80784200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr5:80770200-80794800	Weak transcription	Fetal Brain Female	brain
26	chr5:80770200-80811000	Weak transcription	Colon Smooth Muscle	Colon
27	chr5:80770400-80778000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:80770400-80778000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:80770400-80778400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:80770400-80778600	Weak transcription	Primary T cells from cord blood	blood
31	chr5:80770400-80779400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:80770400-80781400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:80770400-80793600	Weak transcription	Brain Germinal Matrix	brain
34	chr5:80770400-80801600	Weak transcription	Ovary	ovary
35	chr5:80770400-80808200	Weak transcription	Fetal Stomach	stomach
36	chr5:80770600-80778000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr5:80771000-80777800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr5:80771000-80778400	Weak transcription	Fetal Lung	lung
39	chr5:80771000-80780200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr5:80771200-80799600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr5:80773200-80778000	Weak transcription	Dnd41	blood
42	chr5:80773200-80778400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr5:80773400-80786600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr5:80776000-80779200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:80776200-80778800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr5:80776200-80780000	Strong transcription	Fetal Thymus	thymus
47	chr5:80776400-80777800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:80776600-80777200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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