Variant report

Variant	rs2412725
Chromosome Location	chr4:56915247-56915248
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:56914879..56917642-chr4:56927334..56929102,2	MCF-7	breast:
2	chr4:56732780..56733548-chr4:56914397..56915335,2	K562	blood:
3	chr4:56914423..56917343-chr4:56954991..56956586,2	MCF-7	breast:
4	chr4:56902751..56905676-chr4:56913962..56916198,3	MCF-7	breast:
5	chr4:56912197..56914161-chr4:56914438..56916191,2	MCF-7	breast:
6	chr4:56814506..56815307-chr4:56914802..56915691,3	K562	blood:
7	chr4:56910116..56913071-chr4:56914589..56916091,2	MCF-7	breast:
8	chr4:56906651..56909346-chr4:56915136..56917400,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000174799	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10517367	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11938852	0.90[ASN][1000 genomes]
rs13112752	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17086249	0.88[ASN][1000 genomes]
rs2412720	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2412721	0.88[ASN][1000 genomes]
rs2412722	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2412726	0.90[ASN][1000 genomes]
rs2899054	0.88[ASN][1000 genomes]
rs34546346	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34577487	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35976456	0.90[ASN][1000 genomes]
rs36092812	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4355456	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4645275	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59053231	0.88[ASN][1000 genomes]
rs59838410	0.81[ASN][1000 genomes]
rs60296378	0.81[ASN][1000 genomes]
rs6819574	0.88[ASN][1000 genomes]
rs6826903	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6836376	0.83[ASN][1000 genomes]
rs6839870	0.88[ASN][1000 genomes]
rs73155600	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73155601	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73162699	0.89[ASN][1000 genomes]
rs73162701	0.84[ASN][1000 genomes]
rs7672541	0.88[ASN][1000 genomes]
rs7676365	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3378090	chr4:56914220-56916768	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56914000-56916800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr4:56914000-56917000	Active TSS	Cortex derived primary cultured neurospheres	brain
3	chr4:56914000-56917200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr4:56914200-56917000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:56914200-56917200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:56914200-56917400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:56914400-56917000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr4:56914400-56917200	Active TSS	Brain Substantia Nigra	brain
9	chr4:56914400-56917400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr4:56914400-56917800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:56914600-56915400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
12	chr4:56914600-56915600	Active TSS	Brain Germinal Matrix	brain
13	chr4:56914600-56915800	Active TSS	Brain Cingulate Gyrus	brain
14	chr4:56914600-56915800	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr4:56914600-56916200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:56914600-56916400	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr4:56914600-56916400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:56914600-56916600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:56914600-56916600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:56914600-56916600	Active TSS	H9 Cell Line	embryonic stem cell
21	chr4:56914600-56916600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:56914600-56916600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:56914600-56916600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:56914600-56916600	Active TSS	Brain Angular Gyrus	brain
25	chr4:56914600-56916600	Active TSS	Brain Anterior Caudate	brain
26	chr4:56914600-56916600	Active TSS	Brain Hippocampus Middle	brain
27	chr4:56914600-56916600	Active TSS	Rectal Smooth Muscle	rectum
28	chr4:56914600-56916600	Active TSS	NHLF	lung
29	chr4:56914600-56916800	Active TSS	Ovary	ovary
30	chr4:56914600-56917000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:56914600-56917000	Active TSS	Fetal Intestine Large	intestine
32	chr4:56914600-56917000	Active TSS	Fetal Kidney	kidney
33	chr4:56914800-56915400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:56914800-56915400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr4:56914800-56915400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:56914800-56915400	Active TSS	Esophagus	oesophagus
37	chr4:56914800-56915800	Flanking Active TSS	Liver	Liver
38	chr4:56914800-56915800	Bivalent/Poised TSS	Left Ventricle	heart
39	chr4:56914800-56915800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
40	chr4:56914800-56916000	Active TSS	Small Intestine	intestine
41	chr4:56914800-56916200	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr4:56914800-56916200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
43	chr4:56914800-56916200	Active TSS	Aorta	Aorta
44	chr4:56914800-56916200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
45	chr4:56914800-56916200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr4:56914800-56916200	Active TSS	Fetal Lung	lung
47	chr4:56914800-56916400	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr4:56914800-56916400	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr4:56914800-56916400	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr4:56914800-56916600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links