Variant report

Variant	rs12188888
Chromosome Location	chr5:80801869-80801870
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10036712	0.83[ASN][1000 genomes]
rs10042303	0.82[ASN][1000 genomes]
rs10454898	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12153000	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972228	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2972230	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972232	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2972244	0.83[EUR][1000 genomes]
rs2972245	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2973341	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2973343	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2973350	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34414290	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6452416	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6878037	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9293275	0.82[ASN][1000 genomes]
rs964102	0.82[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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80770000-80803000	Weak transcription	Fetal Kidney	kidney
2	chr5:80770000-80811000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:80770000-80812000	Weak transcription	Left Ventricle	heart
4	chr5:80770200-80811000	Weak transcription	Colon Smooth Muscle	Colon
5	chr5:80770400-80808200	Weak transcription	Fetal Stomach	stomach
6	chr5:80779000-80809600	Weak transcription	Primary T cells from cord blood	blood
7	chr5:80779000-80830200	Weak transcription	Primary B cells from cord blood	blood
8	chr5:80779000-80834400	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:80797000-80834000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr5:80797800-80802000	Strong transcription	Dnd41	blood
11	chr5:80798200-80818000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:80798400-80802400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:80798400-80820000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:80798400-80821400	Weak transcription	Thymus	Thymus
15	chr5:80798600-80826600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:80799400-80802400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:80799600-80802800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:80800200-80802600	Enhancers	Brain Substantia Nigra	brain
19	chr5:80800600-80805000	Weak transcription	Fetal Thymus	thymus
20	chr5:80801400-80802000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:80801400-80802000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:80801400-80802200	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr5:80801400-80802600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:80801400-80803000	Enhancers	HUVEC	blood vessel
25	chr5:80801400-80804200	Enhancers	Primary hematopoietic stem cells	blood
26	chr5:80801600-80802000	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr5:80801600-80802000	Active TSS	Brain Hippocampus Middle	brain
28	chr5:80801600-80802000	Active TSS	Ovary	ovary
29	chr5:80801600-80802000	Active TSS	Stomach Smooth Muscle	stomach
30	chr5:80801600-80802000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr5:80801600-80802200	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr5:80801600-80802600	Active TSS	Aorta	Aorta
33	chr5:80801600-80802600	Enhancers	Brain Cingulate Gyrus	brain
34	chr5:80801600-80802600	Active TSS	Right Atrium	heart
35	chr5:80801600-80802600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr5:80801600-80802600	Enhancers	NHLF	lung
37	chr5:80801600-80803200	Enhancers	GM12878-XiMat	blood
38	chr5:80801600-80803600	Enhancers	HSMMtube	muscle
39	chr5:80801800-80802000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:80801800-80802000	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr5:80801800-80802000	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr5:80801800-80802000	Flanking Active TSS	Osteobl	bone
43	chr5:80801800-80802400	Weak transcription	HSMM	muscle
44	chr5:80801800-80802600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:80801800-80802600	Enhancers	Fetal Heart	heart
46	chr5:80801800-80802600	Enhancers	Fetal Lung	lung
47	chr5:80801800-80802800	Enhancers	Liver	Liver

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