Variant report

Variant	rs3924179
Chromosome Location	chr3:48538545-48538546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48538484..48541127-chr3:48554924..48556853,2	MCF-7	breast:
2	chr3:48538275..48540635-chr3:48541463..48544439,2	K562	blood:
3	chr3:48509136..48510838-chr3:48536578..48538592,2	MCF-7	breast:
4	chr3:48504031..48516338-chr3:48532689..48546353,31	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164054	Chromatin interaction
ENSG00000213689	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10780032	1.00[EUR][1000 genomes]
rs11130169	1.00[EUR][1000 genomes]
rs11915428	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858818	1.00[EUR][1000 genomes]
rs55782175	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];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	1.00[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	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7633433	1.00[EUR][1000 genomes]
rs898226	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9852211	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	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

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48514800-48541000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:48515000-48539600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:48515000-48539800	Weak transcription	Osteobl	bone
4	chr3:48515000-48540200	Weak transcription	NHDF-Ad	bronchial
5	chr3:48515000-48540400	Weak transcription	HSMM	muscle
6	chr3:48515000-48541000	Weak transcription	Aorta	Aorta
7	chr3:48515200-48538600	Weak transcription	Small Intestine	intestine
8	chr3:48515200-48539800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:48515200-48540000	Weak transcription	Brain Angular Gyrus	brain
10	chr3:48515200-48540200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:48515200-48540200	Weak transcription	HUVEC	blood vessel
12	chr3:48515200-48540400	Weak transcription	Fetal Brain Female	brain
13	chr3:48515200-48540600	Weak transcription	Brain Germinal Matrix	brain
14	chr3:48515200-48540600	Weak transcription	Fetal Lung	lung
15	chr3:48517200-48540400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:48517200-48540400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:48519600-48538600	Weak transcription	Right Atrium	heart
18	chr3:48519600-48540200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:48519800-48539600	Weak transcription	Right Ventricle	heart
20	chr3:48520800-48540000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:48522200-48539800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:48522400-48539000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:48526600-48540200	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:48527200-48539600	Weak transcription	Left Ventricle	heart
25	chr3:48530600-48540000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr3:48530800-48540400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:48531000-48540600	Weak transcription	A549	lung
28	chr3:48531400-48539000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr3:48531800-48539600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:48532200-48540200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:48532400-48540200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:48532600-48539000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:48533000-48540000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:48533200-48541200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:48533400-48540200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:48533400-48540600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr3:48533600-48539000	Strong transcription	Fetal Intestine Small	intestine
38	chr3:48533600-48539600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:48533800-48538600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:48534000-48538800	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:48534000-48540200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:48534200-48539000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:48534200-48540400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:48534400-48538600	Strong transcription	Lung	lung
45	chr3:48534400-48540200	Weak transcription	NH-A	brain
46	chr3:48534800-48539600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr3:48535000-48539600	Weak transcription	Colonic Mucosa	Colon
48	chr3:48535200-48538800	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:48535200-48539000	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr3:48535200-48540600	Weak transcription	Primary T cells from cord blood	blood

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