Variant report

Variant	rs6452416
Chromosome Location	chr5:80794581-80794582
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80787085..80790084-chr5:80793682..80796599,2	MCF-7	breast:
2	chr5:80789170..80791164-chr5:80794505..80797059,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10036712	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10041030	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10042303	0.83[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs10068144	0.83[ASN][1000 genomes]
rs10075648	1.00[JPT][hapmap]
rs10454898	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10474031	1.00[JPT][hapmap]
rs10942269	1.00[YRI][hapmap]
rs11739075	1.00[JPT][hapmap]
rs12153000	0.80[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12188888	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12697705	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs13159500	0.82[ASN][1000 genomes]
rs13171682	0.81[ASN][1000 genomes]
rs1541830	1.00[JPT][hapmap]
rs2162973	1.00[JPT][hapmap]
rs2972228	0.82[ASN][1000 genomes]
rs2972230	0.80[CEU][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2972232	0.81[CEU][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2972245	0.81[ASN][1000 genomes]
rs2973341	1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2973343	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2973350	0.81[ASN][1000 genomes]
rs34414290	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4392600	1.00[YRI][hapmap]
rs4513668	1.00[YRI][hapmap]
rs6452411	0.93[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6452412	1.00[JPT][hapmap]
rs6452414	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6452415	1.00[JPT][hapmap]
rs6866741	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6868422	1.00[JPT][hapmap]
rs6868748	1.00[JPT][hapmap]
rs6869288	1.00[YRI][hapmap]
rs6871860	1.00[YRI][hapmap]
rs6872775	0.92[JPT][hapmap]
rs6874029	1.00[YRI][hapmap]
rs6877102	1.00[JPT][hapmap]
rs6878037	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6880200	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs6883488	1.00[JPT][hapmap]
rs6887937	1.00[JPT][hapmap]
rs6890850	1.00[YRI][hapmap]
rs6897189	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7702047	1.00[YRI][hapmap]
rs7711020	0.87[JPT][hapmap]
rs7717663	1.00[YRI][hapmap]
rs7719373	1.00[JPT][hapmap]
rs7725320	1.00[YRI][hapmap]
rs7733938	0.93[JPT][hapmap]
rs9293275	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9596	1.00[JPT][hapmap]
rs964102	0.93[JPT][hapmap];0.80[ASN][1000 genomes]

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:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80766200-80800000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:80770000-80797800	Weak transcription	GM12878-XiMat	blood
3	chr5:80770000-80800200	Weak transcription	Brain Anterior Caudate	brain
4	chr5:80770000-80801600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:80770000-80801600	Weak transcription	NHLF	lung
6	chr5:80770000-80803000	Weak transcription	Fetal Kidney	kidney
7	chr5:80770000-80811000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr5:80770000-80812000	Weak transcription	Left Ventricle	heart
9	chr5:80770200-80794800	Weak transcription	Fetal Brain Female	brain
10	chr5:80770200-80811000	Weak transcription	Colon Smooth Muscle	Colon
11	chr5:80770400-80801600	Weak transcription	Ovary	ovary
12	chr5:80770400-80808200	Weak transcription	Fetal Stomach	stomach
13	chr5:80771200-80799600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr5:80778400-80797800	Weak transcription	Thymus	Thymus
15	chr5:80778800-80797800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:80778800-80797800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:80778800-80797800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:80778800-80800400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:80779000-80794800	Weak transcription	Fetal Lung	lung
20	chr5:80779000-80798000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:80779000-80809600	Weak transcription	Primary T cells from cord blood	blood
22	chr5:80779000-80830200	Weak transcription	Primary B cells from cord blood	blood
23	chr5:80779000-80834400	Weak transcription	Fetal Muscle Leg	muscle
24	chr5:80779200-80801800	Weak transcription	Fetal Heart	heart
25	chr5:80782800-80801000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:80783000-80801400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:80785800-80797800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:80787400-80797800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr5:80788400-80801600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr5:80788800-80799600	Weak transcription	Fetal Brain Male	brain
31	chr5:80789800-80797600	Weak transcription	Fetal Thymus	thymus
32	chr5:80790800-80797600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:80791000-80797600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr5:80791400-80801400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:80792600-80795200	Strong transcription	Dnd41	blood
36	chr5:80793200-80801600	Weak transcription	Brain Hippocampus Middle	brain

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