Variant report

Variant	rs2972227
Chromosome Location	chr5:80903830-80903831
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs2917541	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2917543	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2917545	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2921499	0.80[CHB][hapmap]
rs2972237	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972238	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972239	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]
rs2972241	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972245	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2973335	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973336	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2973341	0.81[AFR][1000 genomes]
rs2973345	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2973346	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973347	0.90[CHB][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2973350	1.00[YRI][hapmap]
rs383082	0.88[AMR][1000 genomes]
rs388560	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3943733	0.80[CHB][hapmap]
rs401912	0.90[CHB][hapmap];1.00[CHD][hapmap];0.81[AMR][1000 genomes]
rs402390	0.90[CHB][hapmap]
rs406465	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs433118	0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs433366	0.84[CHD][hapmap]
rs435070	0.84[CHD][hapmap]
rs4426897	1.00[YRI][hapmap]
rs447747	0.87[AMR][1000 genomes]
rs4519906	0.93[ASN][1000 genomes]
rs454578	0.85[CHB][hapmap];1.00[CHD][hapmap]
rs62366265	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6452414	0.81[ASW][hapmap]
rs6452419	1.00[YRI][hapmap]
rs7709916	0.87[CHD][hapmap]
rs827074	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9293275	0.81[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv462222	chr5:80900719-80964452	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv598752	chr5:80900719-80964452	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription 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
rs2972227	CTD-2249K22.1	cis	Thyroid	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80883200-80905800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:80883800-80909200	Weak transcription	HSMM	muscle
3	chr5:80885200-80905400	Weak transcription	Pancreas	Pancrea
4	chr5:80886800-80905400	Weak transcription	Brain Substantia Nigra	brain
5	chr5:80887000-80905600	Weak transcription	Brain Anterior Caudate	brain
6	chr5:80887000-80922400	Weak transcription	Psoas Muscle	Psoas
7	chr5:80887200-80905400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:80887200-80911200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr5:80887400-80904600	Weak transcription	Osteobl	bone
10	chr5:80888600-80905200	Weak transcription	Brain Germinal Matrix	brain
11	chr5:80888600-80905400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:80888800-80905600	Weak transcription	Fetal Stomach	stomach
13	chr5:80892000-80905600	Weak transcription	Gastric	stomach
14	chr5:80892800-80904600	Weak transcription	Fetal Brain Male	brain
15	chr5:80893400-80926000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:80893600-80905600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:80893600-80905600	Weak transcription	Aorta	Aorta
18	chr5:80893600-80909600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr5:80894400-80905200	Weak transcription	Fetal Intestine Large	intestine
20	chr5:80894400-80905400	Weak transcription	Fetal Brain Female	brain
21	chr5:80894400-80905800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr5:80894600-80905600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr5:80894600-80905600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:80894600-80905600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:80894600-80905600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr5:80894600-80905600	Weak transcription	Left Ventricle	heart
27	chr5:80894800-80905400	Weak transcription	Fetal Kidney	kidney
28	chr5:80894800-80905600	Weak transcription	Adipose Nuclei	Adipose
29	chr5:80895000-80905400	Weak transcription	Fetal Muscle Leg	muscle
30	chr5:80895000-80905600	Weak transcription	Brain Hippocampus Middle	brain
31	chr5:80895200-80905400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:80895200-80909600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr5:80895400-80904800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:80895400-80905400	Weak transcription	Liver	Liver
35	chr5:80895400-80905400	Weak transcription	Ovary	ovary
36	chr5:80895600-80909200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr5:80895800-80904600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:80895800-80904800	Weak transcription	Fetal Lung	lung
39	chr5:80895800-80905800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr5:80895800-80912000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:80895800-80922600	Weak transcription	Fetal Heart	heart
42	chr5:80897200-80911800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr5:80897400-80905600	Weak transcription	Esophagus	oesophagus
44	chr5:80897600-80905600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:80897600-80922400	Weak transcription	Colon Smooth Muscle	Colon
46	chr5:80897800-80905600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr5:80898000-80905800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr5:80898400-80910400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr5:80898600-80905400	Weak transcription	Fetal Intestine Small	intestine
50	chr5:80898600-80905600	Weak transcription	Primary monocytes fromperipheralblood	blood

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