Variant report

Variant	rs539782439
Chromosome Location	chr1:45279643-45279644
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45190324..45200952-chr1:45272085..45288310,59	MCF-7	breast:
2	chr1:45193356..45196908-chr1:45277414..45280591,3	MCF-7	breast:
3	chr1:45279599..45282542-chr1:45767964..45769557,2	K562	blood:
4	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
5	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
6	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:

Variant related genes	Relation type
ENSG00000142945	Chromatin interaction
ENSG00000142959	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000234093	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000207421	Chromatin interaction
ENSG00000202031	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
3	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
5	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
6	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
7	nsv461406	chr1:45218542-45293518	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
8	nsv546145	chr1:45218542-45293518	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
9	nsv870815	chr1:45233638-45318752	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
10	nsv546146	chr1:45258141-45318752	Genic enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	109 gene(s)	inside rSNPs	diseases
11	nsv870773	chr1:45259295-45287306	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	108 gene(s)	inside rSNPs	diseases
12	esv3319924	chr1:45278921-45283844	Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
13	esv3445770	chr1:45278947-45283870	Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
14	esv3424987	chr1:45278957-45283908	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
15	esv3319923	chr1:45278961-45283796	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
16	esv3368947	chr1:45279001-45283774	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
17	esv3512041	chr1:45279006-45283809	Active TSS Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
18	esv3512042	chr1:45279006-45283809	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
19	esv3319925	chr1:45279057-45283725	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45275800-45281600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:45276000-45279800	Enhancers	NHDF-Ad	bronchial
3	chr1:45276000-45280600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:45276600-45280600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:45277000-45279800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:45277600-45279800	Enhancers	HUVEC	blood vessel
7	chr1:45277800-45280000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:45277800-45282000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:45278000-45284800	Weak transcription	Hela-S3	cervix
10	chr1:45278200-45284800	Weak transcription	K562	blood
11	chr1:45278400-45280000	Enhancers	Fetal Brain Male	brain
12	chr1:45278400-45280200	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr1:45278600-45279800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr1:45278600-45279800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:45278600-45279800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:45278600-45279800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr1:45278600-45279800	Flanking Active TSS	NH-A	brain
18	chr1:45278600-45280000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr1:45278600-45280800	Weak transcription	HepG2	liver
20	chr1:45278800-45279800	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr1:45278800-45279800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr1:45278800-45279800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:45278800-45279800	Active TSS	H9 Cell Line	embryonic stem cell
24	chr1:45278800-45279800	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr1:45278800-45279800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr1:45278800-45279800	Strong transcription	Aorta	Aorta
27	chr1:45278800-45279800	Active TSS	Brain Angular Gyrus	brain
28	chr1:45278800-45279800	Flanking Active TSS	Colonic Mucosa	Colon
29	chr1:45278800-45279800	Flanking Active TSS	Right Ventricle	heart
30	chr1:45278800-45279800	Active TSS	Stomach Mucosa	stomach
31	chr1:45278800-45280200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:45278800-45280200	Active TSS	Duodenum Mucosa	Duodenum
33	chr1:45278800-45280400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:45278800-45280800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:45278800-45280800	Active TSS	Rectal Smooth Muscle	rectum
36	chr1:45279000-45279800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:45279000-45279800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:45279000-45279800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:45279000-45279800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:45279000-45279800	Active TSS	Brain Cingulate Gyrus	brain
41	chr1:45279000-45279800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:45279000-45279800	Flanking Active TSS	Fetal Muscle Trunk	muscle
43	chr1:45279000-45279800	Transcr. at gene 5' and 3'	Placenta	Placenta
44	chr1:45279000-45280000	Active TSS	H1 Cell Line	embryonic stem cell
45	chr1:45279000-45280000	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr1:45279000-45280000	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr1:45279000-45280000	Active TSS	Brain Germinal Matrix	brain
48	chr1:45279000-45280000	Active TSS	Brain Hippocampus Middle	brain
49	chr1:45279000-45280000	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr1:45279000-45280000	Active TSS	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links