Variant report

Variant	rs73837804
Chromosome Location	chr3:52574012-52574013
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52573995-52574237	U87	brain:	n/a	n/a
2	POLR2A	chr3:52573974-52574271	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52536407..52539525-chr3:52571038..52574825,3	K562	blood:

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

Variant related genes	Relation type
NT5DC2	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10510759	1.00[EUR][1000 genomes]
rs1987234	1.00[EUR][1000 genomes]
rs35920544	1.00[EUR][1000 genomes]
rs56259931	1.00[EUR][1000 genomes]
rs56316289	1.00[AFR][1000 genomes]
rs56960576	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57246324	1.00[EUR][1000 genomes]
rs57319306	1.00[EUR][1000 genomes]
rs57560655	1.00[EUR][1000 genomes]
rs58100002	1.00[EUR][1000 genomes]
rs58409398	1.00[AMR][1000 genomes]
rs58725214	1.00[EUR][1000 genomes]
rs60040519	0.89[AMR][1000 genomes]
rs60256157	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs60415551	1.00[EUR][1000 genomes]
rs60823713	1.00[EUR][1000 genomes]
rs60830326	0.89[AMR][1000 genomes]
rs60916588	1.00[EUR][1000 genomes]
rs72947583	1.00[EUR][1000 genomes]
rs72947584	1.00[EUR][1000 genomes]
rs72947589	1.00[EUR][1000 genomes]
rs72960285	0.89[AMR][1000 genomes]
rs73839126	0.89[AMR][1000 genomes]
rs7648016	1.00[EUR][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	chr3:52571800-52574200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr3:52572200-52574200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:52572200-52574400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:52572200-52574600	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr3:52572200-52575200	Weak transcription	Fetal Kidney	kidney
7	chr3:52572200-52581000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:52572200-52584400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:52572400-52574200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:52572400-52574200	Enhancers	Brain Cingulate Gyrus	brain
11	chr3:52572400-52574200	Enhancers	Right Atrium	heart
12	chr3:52572400-52574200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr3:52572400-52574400	Enhancers	Adipose Nuclei	Adipose
14	chr3:52572400-52578800	Weak transcription	A549	lung
15	chr3:52572400-52580600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:52572400-52581800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:52572400-52594200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:52572400-52633000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:52572600-52574600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:52572800-52574200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:52573000-52574200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:52573000-52574200	Enhancers	Spleen	Spleen
23	chr3:52573000-52574800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:52573000-52574800	Genic enhancers	GM12878-XiMat	blood
25	chr3:52573000-52575000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:52573000-52575400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:52573200-52574200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:52573200-52574200	Genic enhancers	Liver	Liver
29	chr3:52573200-52574200	Strong transcription	Fetal Intestine Small	intestine
30	chr3:52573200-52574200	Strong transcription	Fetal Stomach	stomach
31	chr3:52573200-52574400	Weak transcription	Brain Substantia Nigra	brain
32	chr3:52573200-52575000	Weak transcription	Brain Angular Gyrus	brain
33	chr3:52573200-52575000	Weak transcription	Fetal Intestine Large	intestine
34	chr3:52573200-52575600	Weak transcription	Fetal Lung	lung
35	chr3:52573200-52576200	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:52573200-52576400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr3:52573200-52576600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:52573200-52578600	Weak transcription	Brain Germinal Matrix	brain
39	chr3:52573200-52579000	Weak transcription	Thymus	Thymus
40	chr3:52573200-52582000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:52573200-52583400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:52573200-52585000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:52573200-52586400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:52573200-52589600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:52573200-52590400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:52573400-52574200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr3:52573400-52574200	Genic enhancers	Muscle Satellite Cultured Cells	--
48	chr3:52573400-52574200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:52573400-52574200	Genic enhancers	Left Ventricle	heart
50	chr3:52573400-52574200	Genic enhancers	HUVEC	blood vessel

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