Variant report

Variant	rs6786152
Chromosome Location	chr3:48552834-48552835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TREX1-6	chr3:48550989-48553524	NONHSAT089584

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2098101	1.00[EUR][1000 genomes]
rs28391653	1.00[EUR][1000 genomes]
rs4075800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858794	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs55952796	1.00[EUR][1000 genomes]
rs56073014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56841797	1.00[EUR][1000 genomes]
rs6442128	0.95[AFR][1000 genomes]
rs6783952	0.96[AFR][1000 genomes]
rs6787988	1.00[EUR][1000 genomes]
rs6807104	0.96[AFR][1000 genomes]
rs73831580	1.00[EUR][1000 genomes]
rs73831583	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:83 , 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	chr3:48543000-48556000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:48543000-48556400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:48543000-48556600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:48544000-48561000	Weak transcription	K562	blood
11	chr3:48545000-48559800	Weak transcription	Fetal Intestine Large	intestine
12	chr3:48545200-48558400	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:48545200-48558600	Weak transcription	NHLF	lung
14	chr3:48545200-48572400	Weak transcription	Brain Angular Gyrus	brain
15	chr3:48545400-48554200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:48545400-48554200	Weak transcription	Fetal Intestine Small	intestine
17	chr3:48545400-48555600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:48545400-48555600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:48545400-48556000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:48545400-48556000	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:48545400-48556200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:48545400-48556400	Weak transcription	Brain Anterior Caudate	brain
23	chr3:48545400-48556600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:48545400-48556800	Weak transcription	Brain Substantia Nigra	brain
25	chr3:48545400-48558400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:48545400-48558800	Weak transcription	Gastric	stomach
27	chr3:48545400-48565400	Weak transcription	Pancreas	Pancrea
28	chr3:48545400-48572600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:48545400-48572600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:48545600-48554800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:48545600-48554800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:48545600-48554800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:48545600-48555200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:48545600-48555400	Weak transcription	HepG2	liver
35	chr3:48545600-48555600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:48545600-48555800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr3:48545600-48556200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:48545600-48562600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:48545600-48570600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr3:48545600-48571600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:48545600-48572600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:48546000-48554000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:48546200-48554000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:48546800-48554200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:48546800-48555200	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr3:48547400-48556200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:48547400-48556200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:48547400-48556400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:48547400-48556600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:48547400-48556600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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