Variant report

Variant	rs60823713
Chromosome Location	chr3:52573101-52573102
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52572997-52573628	GM12891	blood:	n/a	n/a
2	TBL1XR1	chr3:52573070-52573156	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:52572992-52573679	Hela-S3	cervix:	n/a	n/a
4	MAFK	chr3:52572840-52573223	K562	blood:	n/a	n/a
5	RCOR1	chr3:52572805-52573311	K562	blood:	n/a	n/a
6	SPI1	chr3:52573016-52573443	HL-60	blood:	n/a	n/a
7	POLR2A	chr3:52572849-52573593	GM12892	blood:	n/a	n/a
8	POLR2A	chr3:52573070-52573526	HepG2	liver:	n/a	n/a
9	SPI1	chr3:52573051-52573301	K562	blood:	n/a	n/a
10	SPI1	chr3:52572949-52573511	HL-60	blood:	n/a	n/a
11	SPI1	chr3:52573044-52573296	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:52572799-52573470	GM12892	blood:	n/a	n/a
13	POLR2A	chr3:52572880-52573288	K562	blood:	n/a	n/a
14	POLR2A	chr3:52572958-52573349	K562	blood:	n/a	n/a
15	POLR2A	chr3:52573079-52573139	HepG2	liver:	n/a	n/a
16	POLR2A	chr3:52572983-52573530	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:52572696-52573730	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:52572688-52573585	GM12878	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52570878..52573539-chr3:52577904..52579826,2	K562	blood:
2	chr3:52536407..52539525-chr3:52571038..52574825,3	K562	blood:
3	chr3:52571791..52573974-chr3:52596279..52597923,2	K562	blood:

No data

Variant related genes	Relation type
NT5DC2	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10510759	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12107484	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1987234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34173244	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35920544	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56156188	0.84[AFR][1000 genomes]
rs56259931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56960576	1.00[EUR][1000 genomes]
rs57008939	0.84[AFR][1000 genomes]
rs57246324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57298447	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57319306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57560655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57757646	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs57869735	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58100002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58725214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58924550	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60311166	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60415551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60611300	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60682984	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60916588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61220667	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61538294	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6445536	0.85[AMR][1000 genomes]
rs6780005	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72947535	0.96[AFR][1000 genomes]
rs72947580	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72947583	1.00[EUR][1000 genomes]
rs72947584	1.00[EUR][1000 genomes]
rs72947589	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950430	0.85[AFR][1000 genomes]
rs72950432	0.83[AFR][1000 genomes]
rs72960240	0.85[AMR][1000 genomes]
rs72960281	0.85[AMR][1000 genomes]
rs72965177	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72965181	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73837804	1.00[EUR][1000 genomes]
rs7619643	0.85[AMR][1000 genomes]
rs7647992	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7648016	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52570000-52573600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr3:52571000-52573400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:52571400-52594200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:52571600-52573400	Enhancers	Primary B cells from peripheral blood	blood
5	chr3:52571600-52573400	Enhancers	Fetal Thymus	thymus
6	chr3:52571600-52573400	Enhancers	Small Intestine	intestine
7	chr3:52571600-52573600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:52571600-52573600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
9	chr3:52571800-52573200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:52571800-52573400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:52571800-52573600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:52571800-52573800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:52571800-52574200	Enhancers	Primary T cells fromperipheralblood	blood
14	chr3:52572000-52573200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr3:52572000-52573200	Enhancers	H9 Cell Line	embryonic stem cell
16	chr3:52572000-52573400	Enhancers	Fetal Brain Male	brain
17	chr3:52572000-52573600	Enhancers	Primary hematopoietic stem cells	blood
18	chr3:52572000-52573600	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr3:52572000-52573600	Enhancers	Esophagus	oesophagus
20	chr3:52572000-52573600	Genic enhancers	Fetal Muscle Leg	muscle
21	chr3:52572000-52573600	Enhancers	Placenta	Placenta
22	chr3:52572000-52573600	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr3:52572000-52574000	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr3:52572200-52573200	Enhancers	Brain Germinal Matrix	brain
25	chr3:52572200-52573200	Enhancers	Brain Substantia Nigra	brain
26	chr3:52572200-52573200	Enhancers	Fetal Lung	lung
27	chr3:52572200-52573200	Enhancers	Thymus	Thymus
28	chr3:52572200-52573400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:52572200-52573400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:52572200-52573400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:52572200-52573400	Enhancers	Stomach Mucosa	stomach
32	chr3:52572200-52573600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:52572200-52573600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr3:52572200-52573600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:52572200-52573600	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr3:52572200-52573600	Enhancers	Colon Smooth Muscle	Colon
37	chr3:52572200-52573800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:52572200-52573800	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr3:52572200-52574200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:52572200-52574400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:52572200-52574600	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr3:52572200-52575200	Weak transcription	Fetal Kidney	kidney
43	chr3:52572200-52581000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:52572200-52584400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:52572400-52573200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr3:52572400-52573200	Weak transcription	Aorta	Aorta
47	chr3:52572400-52573200	Enhancers	Liver	Liver
48	chr3:52572400-52573200	Enhancers	Brain Angular Gyrus	brain
49	chr3:52572400-52573200	Enhancers	Duodenum Mucosa	Duodenum
50	chr3:52572400-52573200	Enhancers	Fetal Intestine Large	intestine

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