Variant report

Variant	rs2972236
Chromosome Location	chr5:80833733-80833734
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11746820	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11747523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13159526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13173067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13180125	0.83[CEU][hapmap];0.89[AFR][1000 genomes]
rs13184667	0.89[AFR][1000 genomes]
rs2917540	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2972231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972243	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972246	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973340	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973348	0.95[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2973349	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3916011	0.89[AFR][1000 genomes]
rs396231	0.82[CHB][hapmap]
rs4607338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898782	0.82[CHB][hapmap]
rs71636275	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.93[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:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80779000-80834400	Weak transcription	Fetal Muscle Leg	muscle
2	chr5:80797000-80834000	Weak transcription	Primary B cells from peripheral blood	blood
3	chr5:80803200-80834400	Weak transcription	Fetal Kidney	kidney
4	chr5:80803200-80835200	Weak transcription	GM12878-XiMat	blood
5	chr5:80803600-80875200	Weak transcription	Fetal Brain Female	brain
6	chr5:80820200-80851800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:80820800-80834600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:80821800-80836800	Weak transcription	NHDF-Ad	bronchial
9	chr5:80821800-80849000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:80825200-80865200	Weak transcription	Fetal Brain Male	brain
11	chr5:80827000-80840600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:80827000-80848200	Weak transcription	Left Ventricle	heart
13	chr5:80827600-80835600	Enhancers	Primary T cells from cord blood	blood
14	chr5:80828400-80834400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:80828800-80863400	Weak transcription	Fetal Lung	lung
16	chr5:80830000-80848800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr5:80830000-80853800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:80830200-80848600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr5:80830400-80845000	Weak transcription	Fetal Heart	heart
20	chr5:80830600-80840200	Weak transcription	Primary B cells from cord blood	blood
21	chr5:80830600-80841400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:80830800-80849600	Weak transcription	Adipose Nuclei	Adipose
23	chr5:80830800-80850000	Weak transcription	Colon Smooth Muscle	Colon
24	chr5:80831000-80834200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr5:80831000-80845200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:80831800-80834200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:80832000-80835600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr5:80832400-80834000	Genic enhancers	Dnd41	blood
29	chr5:80832600-80834000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:80833000-80835000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr5:80833000-80835000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr5:80833000-80835000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr5:80833000-80835200	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr5:80833000-80835200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr5:80833000-80835400	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr5:80833200-80833800	Enhancers	Stomach Mucosa	stomach
37	chr5:80833200-80834400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:80833200-80835000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr5:80833200-80835000	Enhancers	Fetal Thymus	thymus
40	chr5:80833200-80835200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr5:80833200-80835600	Enhancers	Thymus	Thymus
42	chr5:80833400-80833800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr5:80833400-80834400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr5:80833600-80834200	Enhancers	Primary T cells fromperipheralblood	blood
45	chr5:80833600-80835400	Enhancers	Primary T killer memory cells from peripheral blood	blood

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