Variant report

Variant	rs55782175
Chromosome Location	chr3:48549535-48549536
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TREX1-5	chr3:48547829-48550227	NONHSAT089582

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10780032	1.00[EUR][1000 genomes]
rs11130169	1.00[EUR][1000 genomes]
rs11915428	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3924179	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858818	1.00[EUR][1000 genomes]
rs58708931	1.00[EUR][1000 genomes]
rs58835493	1.00[EUR][1000 genomes]
rs59352296	1.00[EUR][1000 genomes]
rs60352528	1.00[EUR][1000 genomes]
rs6442122	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6762888	0.92[AFR][1000 genomes]
rs6791777	1.00[EUR][1000 genomes]
rs6793732	1.00[EUR][1000 genomes]
rs6801348	1.00[EUR][1000 genomes]
rs73830466	1.00[EUR][1000 genomes]
rs73830478	1.00[EUR][1000 genomes]
rs73831565	1.00[EUR][1000 genomes]
rs73831572	1.00[EUR][1000 genomes]
rs73831577	1.00[EUR][1000 genomes]
rs73831579	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7633433	1.00[EUR][1000 genomes]
rs898226	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9852211	1.00[EUR][1000 genomes]
rs9860187	1.00[EUR][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	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1802114	chr3:48498822-48577670	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48542600-48554800	Weak transcription	Fetal Brain Female	brain
2	chr3:48542800-48554000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:48542800-48554800	Weak transcription	Brain Germinal Matrix	brain
4	chr3:48542800-48558200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:48542800-48562800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:48542800-48569800	Weak transcription	Right Atrium	heart
7	chr3:48543000-48549600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:48543000-48556000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:48543000-48556400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:48543000-48556600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:48544000-48561000	Weak transcription	K562	blood
12	chr3:48545000-48559800	Weak transcription	Fetal Intestine Large	intestine
13	chr3:48545200-48558400	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:48545200-48558600	Weak transcription	NHLF	lung
15	chr3:48545200-48572400	Weak transcription	Brain Angular Gyrus	brain
16	chr3:48545400-48554200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:48545400-48554200	Weak transcription	Fetal Intestine Small	intestine
18	chr3:48545400-48555600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:48545400-48555600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:48545400-48556000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:48545400-48556000	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:48545400-48556200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:48545400-48556400	Weak transcription	Brain Anterior Caudate	brain
24	chr3:48545400-48556600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:48545400-48556800	Weak transcription	Brain Substantia Nigra	brain
26	chr3:48545400-48558400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:48545400-48558800	Weak transcription	Gastric	stomach
28	chr3:48545400-48565400	Weak transcription	Pancreas	Pancrea
29	chr3:48545400-48572600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:48545400-48572600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:48545600-48549600	Weak transcription	Primary T cells from cord blood	blood
32	chr3:48545600-48549800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:48545600-48550800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:48545600-48550800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:48545600-48551200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr3:48545600-48552000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:48545600-48552200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:48545600-48554800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:48545600-48554800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:48545600-48554800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr3:48545600-48555200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:48545600-48555400	Weak transcription	HepG2	liver
43	chr3:48545600-48555600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:48545600-48555800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr3:48545600-48556200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:48545600-48562600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:48545600-48570600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:48545600-48571600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:48545600-48572600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:48545800-48549600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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