Variant report

Variant	rs2973335
Chromosome Location	chr5:80904933-80904934
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10942269	0.85[LWK][hapmap]
rs2917541	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2917543	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2917545	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2921499	0.80[CHB][hapmap]
rs2972227	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]
rs2972237	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972238	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972239	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]
rs2972241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972245	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2973336	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];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2973341	0.87[ASW][hapmap];0.83[LWK][hapmap];0.81[AFR][1000 genomes]
rs2973345	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2973346	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973347	1.00[ASW][hapmap];0.90[CHB][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2973350	1.00[YRI][hapmap]
rs369382	0.80[AMR][1000 genomes]
rs383082	0.87[AMR][1000 genomes]
rs388560	1.00[AFR][1000 genomes];0.96[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];0.84[MEX][hapmap];0.80[AMR][1000 genomes]
rs402390	0.90[CHB][hapmap];0.80[AMR][1000 genomes]
rs406465	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs417684	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[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];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs433366	0.84[CHD][hapmap]
rs435070	0.84[CHD][hapmap]
rs4426897	1.00[YRI][hapmap]
rs447747	0.88[AMR][1000 genomes]
rs4513668	0.85[LWK][hapmap]
rs4519906	0.93[ASN][1000 genomes]
rs454578	0.85[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes]
rs62366265	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6452419	1.00[YRI][hapmap]
rs6874029	0.85[LWK][hapmap]
rs7709916	0.87[CHD][hapmap]
rs827074	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2973335	CTD-2249K22.1	cis	Thyroid	GTEx
rs2973335	HOMER1	cis	parietal	SCAN

Chromatin state (count:87 , 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	chr5:80888600-80905200	Weak transcription	Brain Germinal Matrix	brain
10	chr5:80888600-80905400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:80888800-80905600	Weak transcription	Fetal Stomach	stomach
12	chr5:80892000-80905600	Weak transcription	Gastric	stomach
13	chr5:80893400-80926000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr5:80893600-80905600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr5:80893600-80905600	Weak transcription	Aorta	Aorta
16	chr5:80893600-80909600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr5:80894400-80905200	Weak transcription	Fetal Intestine Large	intestine
18	chr5:80894400-80905400	Weak transcription	Fetal Brain Female	brain
19	chr5:80894400-80905800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr5:80894600-80905600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr5:80894600-80905600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:80894600-80905600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:80894600-80905600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr5:80894600-80905600	Weak transcription	Left Ventricle	heart
25	chr5:80894800-80905400	Weak transcription	Fetal Kidney	kidney
26	chr5:80894800-80905600	Weak transcription	Adipose Nuclei	Adipose
27	chr5:80895000-80905400	Weak transcription	Fetal Muscle Leg	muscle
28	chr5:80895000-80905600	Weak transcription	Brain Hippocampus Middle	brain
29	chr5:80895200-80905400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:80895200-80909600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr5:80895400-80905400	Weak transcription	Liver	Liver
32	chr5:80895400-80905400	Weak transcription	Ovary	ovary
33	chr5:80895600-80909200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr5:80895800-80905800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr5:80895800-80912000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr5:80895800-80922600	Weak transcription	Fetal Heart	heart
37	chr5:80897200-80911800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr5:80897400-80905600	Weak transcription	Esophagus	oesophagus
39	chr5:80897600-80905600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:80897600-80922400	Weak transcription	Colon Smooth Muscle	Colon
41	chr5:80897800-80905600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr5:80898000-80905800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr5:80898400-80910400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr5:80898600-80905400	Weak transcription	Fetal Intestine Small	intestine
45	chr5:80898600-80905600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr5:80899200-80905600	Weak transcription	Lung	lung
47	chr5:80899400-80905200	Weak transcription	Primary B cells from peripheral blood	blood
48	chr5:80899400-80905600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:80899400-80905600	Weak transcription	HSMMtube	muscle
50	chr5:80899400-80905600	Weak transcription	Monocytes-CD14+_RO01746	blood

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