Variant report

Variant	rs55971019
Chromosome Location	chr3:52574808-52574809
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52536407..52539525-chr3:52571038..52574825,3	K562	blood:
2	chr3:52574434..52577960-chr3:52578839..52582098,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NT5DC2-1	chr3:52573952-52575907	ENSG00000245797

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17052329	0.90[AFR][1000 genomes]
rs3890123	1.00[AMR][1000 genomes]
rs56898787	1.00[AMR][1000 genomes]
rs56961704	1.00[AMR][1000 genomes]
rs58781613	1.00[AMR][1000 genomes]
rs59277755	0.84[AFR][1000 genomes]
rs60499166	1.00[AMR][1000 genomes]
rs60997031	1.00[AMR][1000 genomes]
rs61734628	1.00[AMR][1000 genomes]
rs6766038	1.00[AMR][1000 genomes]
rs73837049	1.00[AMR][1000 genomes]
rs73837599	1.00[AMR][1000 genomes]
rs73838354	1.00[AMR][1000 genomes]
rs73839116	1.00[AMR][1000 genomes]
rs73839117	1.00[AMR][1000 genomes]
rs73839167	0.84[AFR][1000 genomes]
rs7638914	1.00[AMR][1000 genomes]
rs7641255	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52571400-52594200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:52572200-52575200	Weak transcription	Fetal Kidney	kidney
3	chr3:52572200-52581000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:52572200-52584400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:52572400-52578800	Weak transcription	A549	lung
6	chr3:52572400-52580600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:52572400-52581800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:52572400-52594200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:52572400-52633000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:52573000-52575000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:52573000-52575400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:52573200-52575000	Weak transcription	Brain Angular Gyrus	brain
13	chr3:52573200-52575000	Weak transcription	Fetal Intestine Large	intestine
14	chr3:52573200-52575600	Weak transcription	Fetal Lung	lung
15	chr3:52573200-52576200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:52573200-52576400	Strong transcription	Fetal Muscle Trunk	muscle
17	chr3:52573200-52576600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:52573200-52578600	Weak transcription	Brain Germinal Matrix	brain
19	chr3:52573200-52579000	Weak transcription	Thymus	Thymus
20	chr3:52573200-52582000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:52573200-52583400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:52573200-52585000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:52573200-52586400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:52573200-52589600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:52573200-52590400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:52573400-52575000	Weak transcription	Primary B cells from cord blood	blood
27	chr3:52573400-52575000	Weak transcription	Fetal Heart	heart
28	chr3:52573400-52575000	Weak transcription	HSMMtube	muscle
29	chr3:52573400-52575600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:52573400-52575800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:52573400-52575800	Strong transcription	NHDF-Ad	bronchial
32	chr3:52573400-52576000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:52573400-52576000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:52573400-52576200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:52573400-52576200	Strong transcription	NHLF	lung
36	chr3:52573400-52580600	Weak transcription	Fetal Brain Male	brain
37	chr3:52573400-52585200	Weak transcription	Small Intestine	intestine
38	chr3:52573400-52595000	Weak transcription	Stomach Mucosa	stomach
39	chr3:52573600-52575000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:52573600-52575000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:52573600-52575000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:52573600-52575000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:52573600-52575000	Weak transcription	Colon Smooth Muscle	Colon
44	chr3:52573600-52575000	Weak transcription	Gastric	stomach
45	chr3:52573600-52575000	Weak transcription	Lung	lung
46	chr3:52573600-52575000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:52573600-52575000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr3:52573600-52575200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:52573600-52575200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:52573600-52575800	Strong transcription	Rectal Mucosa Donor 29	rectum

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