Variant report

Variant	rs406465
Chromosome Location	chr5:80926269-80926270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10942269	0.85[LWK][hapmap]
rs2917541	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2917543	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2917545	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[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];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2921499	0.85[CHB][hapmap]
rs2972227	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]
rs2972237	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2972238	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972239	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]
rs2972241	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2972245	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2973335	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]
rs2973336	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[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];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973346	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2973347	1.00[ASW][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2973350	1.00[YRI][hapmap]
rs383082	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs388560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3943733	0.85[CHB][hapmap];0.84[MEX][hapmap]
rs401912	0.84[CHB][hapmap];0.97[CHD][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes]
rs402390	0.84[CHB][hapmap]
rs417684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs433118	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs433366	0.81[CHD][hapmap]
rs435070	0.81[CHD][hapmap]
rs4426897	1.00[YRI][hapmap]
rs447747	0.89[AMR][1000 genomes]
rs4513668	0.85[LWK][hapmap]
rs4519906	0.92[ASN][1000 genomes]
rs454578	0.90[CHB][hapmap];0.97[CHD][hapmap];0.90[MEX][hapmap]
rs62366265	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6452419	1.00[YRI][hapmap]
rs6874029	0.85[LWK][hapmap]
rs7709916	0.84[CHD][hapmap]
rs827074	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	nsv882235	chr5:80909132-81006061	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats 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
7	nsv830361	chr5:80909811-81080409	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs406465	CTD-2249K22.1	cis	Thyroid	GTEx
rs406465	HOMER1	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80906000-80927000	Weak transcription	Gastric	stomach
2	chr5:80906000-80929400	Weak transcription	Fetal Brain Female	brain
3	chr5:80906000-80935000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:80906000-80946600	Weak transcription	Brain Anterior Caudate	brain
5	chr5:80906000-80947000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:80906200-80926600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr5:80906200-80927000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr5:80906200-80927200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:80906200-80927600	Weak transcription	Lung	lung
10	chr5:80906200-80930600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr5:80906200-80933000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr5:80906200-80938800	Weak transcription	Left Ventricle	heart
13	chr5:80906200-80942400	Weak transcription	Esophagus	oesophagus
14	chr5:80906200-80947800	Weak transcription	Brain Germinal Matrix	brain
15	chr5:80906600-80936200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:80909600-80926600	Weak transcription	Primary T cells from cord blood	blood
17	chr5:80909600-80933200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:80910000-80930600	Weak transcription	Adipose Nuclei	Adipose
19	chr5:80910400-80953000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr5:80910800-80949200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr5:80918200-80934800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr5:80918400-80938800	Weak transcription	Fetal Stomach	stomach
23	chr5:80918400-80939800	Weak transcription	Fetal Lung	lung
24	chr5:80918800-80935200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr5:80920600-80946800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr5:80921200-80927000	Weak transcription	Small Intestine	intestine
27	chr5:80921200-80983000	Weak transcription	Aorta	Aorta
28	chr5:80922600-80929400	Weak transcription	Fetal Muscle Leg	muscle
29	chr5:80922600-80933600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr5:80922600-80935800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:80922600-80937600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr5:80922800-80934600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:80922800-80935000	Weak transcription	Colon Smooth Muscle	Colon
34	chr5:80923000-80952800	Weak transcription	Fetal Intestine Large	intestine
35	chr5:80923200-80927400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr5:80923200-80929800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:80923200-80930600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:80923200-80934200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:80923200-80934400	Weak transcription	NHDF-Ad	bronchial
40	chr5:80923200-80942000	Weak transcription	Fetal Intestine Small	intestine
41	chr5:80923200-80947000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr5:80923200-80948400	Weak transcription	K562	blood
43	chr5:80923400-80927000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr5:80923400-80930400	Weak transcription	Fetal Heart	heart
45	chr5:80923400-80934600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:80923400-80934600	Weak transcription	NHLF	lung
47	chr5:80923400-80934600	Weak transcription	Osteobl	bone
48	chr5:80923400-80938400	Weak transcription	HUVEC	blood vessel
49	chr5:80923600-80926400	Genic enhancers	Fetal Thymus	thymus
50	chr5:80923600-80927800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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