Variant report

Variant	rs55754265
Chromosome Location	chr3:49687486-49687487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49576104..49578514-chr3:49684857..49687792,2	MCF-7	breast:
2	chr3:49686939..49689819-chr3:49694987..49697482,3	K562	blood:
3	chr3:49687205..49689854-chr3:49709727..49711348,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10452032	0.81[EUR][1000 genomes]
rs1078341	0.81[EUR][1000 genomes]
rs13096480	0.81[EUR][1000 genomes]
rs1352889	0.81[EUR][1000 genomes]
rs1586827	0.81[EUR][1000 genomes]
rs2131108	0.81[EUR][1000 genomes]
rs2329021	0.81[EUR][1000 genomes]
rs4855833	0.81[EUR][1000 genomes]
rs4855845	0.81[EUR][1000 genomes]
rs4855846	0.81[EUR][1000 genomes]
rs4855848	0.81[EUR][1000 genomes]
rs4855849	0.81[EUR][1000 genomes]
rs4855885	0.80[EUR][1000 genomes]
rs62262671	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62262672	0.81[EUR][1000 genomes]
rs62262673	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62262675	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6446286	0.81[EUR][1000 genomes]
rs9824435	0.81[EUR][1000 genomes]
rs9830730	0.81[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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55754265	AMT	cis	Thyroid	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49661600-49692400	Weak transcription	Ovary	ovary
2	chr3:49669400-49692000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:49673800-49692400	Weak transcription	Gastric	stomach
4	chr3:49675400-49688200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:49676200-49692000	Weak transcription	Esophagus	oesophagus
6	chr3:49679800-49687600	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr3:49681200-49688600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:49681200-49688800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:49682200-49689000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:49682600-49688400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:49684600-49687800	Genic enhancers	Brain Inferior Temporal Lobe	brain
12	chr3:49684800-49687600	Enhancers	Psoas Muscle	Psoas
13	chr3:49684800-49688000	Enhancers	HepG2	liver
14	chr3:49684800-49688400	Enhancers	Fetal Muscle Leg	muscle
15	chr3:49684800-49688800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr3:49684800-49689400	Enhancers	Fetal Muscle Trunk	muscle
17	chr3:49685000-49687600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:49685200-49708200	Strong transcription	Brain Germinal Matrix	brain
19	chr3:49685400-49687600	Enhancers	K562	blood
20	chr3:49685400-49690400	Weak transcription	Lung	lung
21	chr3:49685400-49708400	Strong transcription	Fetal Brain Female	brain
22	chr3:49685600-49693200	Weak transcription	Liver	Liver
23	chr3:49685800-49688400	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:49685800-49688400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:49685800-49689000	Weak transcription	Fetal Stomach	stomach
26	chr3:49685800-49689600	Weak transcription	Brain Substantia Nigra	brain
27	chr3:49685800-49692600	Weak transcription	Fetal Intestine Small	intestine
28	chr3:49686000-49687600	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr3:49686000-49688400	Weak transcription	Brain Anterior Caudate	brain
30	chr3:49686000-49689000	Weak transcription	Brain Angular Gyrus	brain
31	chr3:49686000-49692400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:49686000-49692600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:49686400-49687600	Enhancers	Spleen	Spleen
34	chr3:49686400-49687800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:49686600-49688200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:49686600-49697200	Weak transcription	Pancreas	Pancrea
37	chr3:49686600-49710600	Weak transcription	Right Atrium	heart
38	chr3:49686800-49687800	Enhancers	Primary hematopoietic stem cells	blood
39	chr3:49687000-49687600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:49687000-49687600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:49687000-49687600	Enhancers	Right Ventricle	heart
42	chr3:49687000-49687600	Enhancers	HMEC	breast
43	chr3:49687000-49687800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:49687000-49687800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:49687000-49687800	Enhancers	Fetal Thymus	thymus
46	chr3:49687000-49688600	Enhancers	GM12878-XiMat	blood
47	chr3:49687000-49695600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:49687400-49687800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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