Variant report

Variant	rs2972239
Chromosome Location	chr5:80887552-80887553
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs2917541	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2917543	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2917545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2921499	0.81[CHB][hapmap]
rs2972227	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972237	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972238	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972241	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2972245	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2973335	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2973336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2973341	0.81[AFR][1000 genomes]
rs2973345	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2973346	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2973347	0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2973350	1.00[YRI][hapmap]
rs383082	0.85[AMR][1000 genomes]
rs388560	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3943733	0.80[CHB][hapmap]
rs401912	0.90[CHB][hapmap]
rs402390	0.90[CHB][hapmap]
rs406465	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs417684	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs433118	0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4426897	1.00[YRI][hapmap]
rs447747	0.86[AMR][1000 genomes]
rs4519906	0.94[ASN][1000 genomes]
rs454578	0.85[CHB][hapmap]
rs62366265	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6452419	1.00[YRI][hapmap]
rs827074	0.85[AMR][1000 genomes];0.86[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
rs2972239	CTD-2249K22.1	cis	Thyroid	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80864200-80894200	Weak transcription	Fetal Lung	lung
2	chr5:80864600-80894200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr5:80869400-80887600	Weak transcription	Fetal Stomach	stomach
4	chr5:80870000-80887600	Weak transcription	Aorta	Aorta
5	chr5:80870800-80894200	Weak transcription	Primary B cells from cord blood	blood
6	chr5:80875600-80894000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:80875600-80894200	Weak transcription	GM12878-XiMat	blood
8	chr5:80876000-80894200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr5:80879000-80887600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:80881400-80894200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr5:80882800-80888000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:80883200-80887600	Weak transcription	Brain Germinal Matrix	brain
13	chr5:80883200-80905800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr5:80883800-80909200	Weak transcription	HSMM	muscle
15	chr5:80885000-80894200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:80885200-80905400	Weak transcription	Pancreas	Pancrea
17	chr5:80885800-80887800	Enhancers	Dnd41	blood
18	chr5:80886200-80888600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr5:80886400-80888800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:80886800-80905400	Weak transcription	Brain Substantia Nigra	brain
21	chr5:80887000-80887600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:80887000-80888400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:80887000-80894400	Weak transcription	Left Ventricle	heart
24	chr5:80887000-80905600	Weak transcription	Brain Anterior Caudate	brain
25	chr5:80887000-80922400	Weak transcription	Psoas Muscle	Psoas
26	chr5:80887200-80887600	Weak transcription	Fetal Thymus	thymus
27	chr5:80887200-80887800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
28	chr5:80887200-80894200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:80887200-80894200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr5:80887200-80894400	Weak transcription	Primary T cells from cord blood	blood
31	chr5:80887200-80894400	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr5:80887200-80894400	Weak transcription	Thymus	Thymus
33	chr5:80887200-80898000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr5:80887200-80905400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr5:80887200-80911200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr5:80887400-80887600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
37	chr5:80887400-80904600	Weak transcription	Osteobl	bone

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