Variant report

Variant	rs55774261
Chromosome Location	chr5:178151343-178151344
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10043035	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1071881	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1071882	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1071883	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1079487	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1132336	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1132338	0.80[AMR][1000 genomes]
rs11739893	0.82[EUR][1000 genomes]
rs11740283	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11742156	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11742176	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11742808	0.82[EUR][1000 genomes]
rs11743893	0.81[EUR][1000 genomes]
rs11747097	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11747232	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11747390	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11748495	0.82[EUR][1000 genomes]
rs11748497	0.82[EUR][1000 genomes]
rs11749438	0.82[EUR][1000 genomes]
rs11750409	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11750784	0.84[AMR][1000 genomes]
rs13173130	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13186580	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17184281	0.81[EUR][1000 genomes]
rs17184302	0.82[EUR][1000 genomes]
rs17184344	0.82[EUR][1000 genomes]
rs17652247	0.82[EUR][1000 genomes]
rs34601045	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34645905	0.81[AMR][1000 genomes]
rs34651317	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34703961	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34981407	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35007468	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35850587	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4266420	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4470778	0.85[EUR][1000 genomes]
rs4533908	0.81[AMR][1000 genomes]
rs55818572	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55974982	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56027952	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56070635	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56159071	0.81[EUR][1000 genomes]
rs56206101	0.82[EUR][1000 genomes]
rs56236920	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58549512	0.82[EUR][1000 genomes]
rs59259518	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61247551	0.82[EUR][1000 genomes]
rs62392825	0.82[EUR][1000 genomes]
rs62392831	0.82[EUR][1000 genomes]
rs62392832	0.82[EUR][1000 genomes]
rs62392833	0.82[EUR][1000 genomes]
rs62392839	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62392842	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62392852	0.86[ASN][1000 genomes]
rs62392854	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66947564	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6870021	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6873150	0.81[EUR][1000 genomes]
rs6890741	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6896799	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71611460	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72812613	0.81[EUR][1000 genomes]
rs7732764	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv883217	chr5:178099758-178193081	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1031206	chr5:178149292-178283614	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537973	chr5:178149292-178283614	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv964986	chr5:178150596-178151568	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55774261	ZNF354A	cis	Thyroid	GTEx
rs55774261	ZNF354A	cis	Whole Blood	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178135800-178155600	ZNF genes & repeats	Liver	Liver
2	chr5:178136200-178155200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr5:178136800-178152800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr5:178138400-178155600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:178138800-178154400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr5:178138800-178155600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:178139000-178154000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
8	chr5:178139400-178154800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:178139600-178152800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
10	chr5:178139800-178152600	ZNF genes & repeats	Ovary	ovary
11	chr5:178139800-178153400	ZNF genes & repeats	Brain Germinal Matrix	brain
12	chr5:178139800-178153400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
13	chr5:178139800-178154800	ZNF genes & repeats	Fetal Intestine Large	intestine
14	chr5:178140600-178156600	Weak transcription	Hela-S3	cervix
15	chr5:178140800-178156000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
16	chr5:178141000-178151600	ZNF genes & repeats	Aorta	Aorta
17	chr5:178141000-178155000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:178141000-178155200	ZNF genes & repeats	Lung	lung
19	chr5:178141800-178153800	ZNF genes & repeats	Spleen	Spleen
20	chr5:178141800-178155600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:178142800-178155600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:178143200-178154200	ZNF genes & repeats	Gastric	stomach
23	chr5:178144600-178154800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:178144600-178155600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:178145400-178153800	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr5:178145400-178155400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr5:178146000-178152200	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr5:178146000-178154400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:178147600-178153800	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr5:178147600-178155200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr5:178147800-178155400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr5:178148000-178155400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr5:178148000-178155600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr5:178148000-178155600	Strong transcription	Right Ventricle	heart
35	chr5:178148400-178154200	ZNF genes & repeats	Thymus	Thymus
36	chr5:178148400-178154800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:178148400-178156600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr5:178148600-178153600	ZNF genes & repeats	Fetal Stomach	stomach
39	chr5:178148600-178154000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr5:178148800-178155600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr5:178149000-178152000	Weak transcription	NHDF-Ad	bronchial
42	chr5:178149200-178152200	Strong transcription	Primary T cells from cord blood	blood
43	chr5:178149200-178154200	Strong transcription	Dnd41	blood
44	chr5:178149200-178156400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr5:178149400-178152000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr5:178149400-178152200	Strong transcription	A549	lung
47	chr5:178149400-178154600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr5:178149400-178155000	Strong transcription	Colon Smooth Muscle	Colon
49	chr5:178149400-178155400	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr5:178149400-178156600	Weak transcription	Stomach Mucosa	stomach

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