Variant report

Variant	rs2972238
Chromosome Location	chr5:80885073-80885074
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs2917541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2917543	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2917545	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2972227	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972237	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972239	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972245	0.86[AFR][1000 genomes]
rs2973335	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2973336	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973341	0.81[AFR][1000 genomes]
rs2973345	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2973346	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2973347	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs383082	0.87[AMR][1000 genomes]
rs388560	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs406465	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs417684	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs433118	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs447747	0.86[AMR][1000 genomes]
rs4519906	0.94[ASN][1000 genomes]
rs62366265	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs827074	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882233	chr5:80849084-81049187	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv882234	chr5:80853708-80966666	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv525437	chr5:80876359-80964452	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2972238	CTD-2249K22.1	cis	Thyroid	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80849000-80885600	Weak transcription	Left Ventricle	heart
2	chr5:80864200-80886400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:80864200-80894200	Weak transcription	Fetal Lung	lung
4	chr5:80864600-80894200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr5:80869400-80887600	Weak transcription	Fetal Stomach	stomach
6	chr5:80869800-80886400	Weak transcription	Thymus	Thymus
7	chr5:80870000-80887600	Weak transcription	Aorta	Aorta
8	chr5:80870600-80886600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:80870800-80894200	Weak transcription	Primary B cells from cord blood	blood
10	chr5:80875600-80886800	Weak transcription	Brain Anterior Caudate	brain
11	chr5:80875600-80894000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:80875600-80894200	Weak transcription	GM12878-XiMat	blood
13	chr5:80876000-80885600	Weak transcription	Primary T cells from cord blood	blood
14	chr5:80876000-80894200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr5:80877200-80885800	Weak transcription	Dnd41	blood
16	chr5:80879000-80887600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:80881400-80886200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr5:80881400-80894200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr5:80882200-80886800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:80882800-80886200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr5:80882800-80888000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:80883000-80885600	Strong transcription	Fetal Thymus	thymus
23	chr5:80883200-80887600	Weak transcription	Brain Germinal Matrix	brain
24	chr5:80883200-80905800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr5:80883400-80886600	Weak transcription	Psoas Muscle	Psoas
26	chr5:80883400-80886600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr5:80883600-80886400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:80883800-80909200	Weak transcription	HSMM	muscle
29	chr5:80884600-80885400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr5:80884600-80885800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:80884800-80885600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr5:80884800-80886800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:80885000-80894200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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