Variant report

Variant	rs4423869
Chromosome Location	chr4:15491851-15491852
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15479756..15482166-chr4:15489455..15493787,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000048342	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10000250	0.93[CEU][hapmap]
rs10022530	1.00[CEU][hapmap]
rs1024760	0.86[CEU][hapmap]
rs4698382	0.86[CEU][hapmap]
rs719993	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs9990934	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs9993580	1.00[CEU][hapmap]
rs9994702	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers 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	23 gene(s)	inside rSNPs	diseases
4	nsv966255	chr4:15490773-15496105	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4423869	CC2D2A,DKFZp547J222	cis	brain	BrainEAC

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15481600-15498600	Weak transcription	Liver	Liver
2	chr4:15481600-15519000	Weak transcription	Gastric	stomach
3	chr4:15482200-15519800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:15482600-15516600	Weak transcription	Brain Angular Gyrus	brain
5	chr4:15482600-15526400	Weak transcription	HMEC	breast
6	chr4:15482800-15518200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:15483600-15493400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:15483600-15498600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:15485000-15504800	Weak transcription	Ovary	ovary
10	chr4:15485200-15494400	Weak transcription	Fetal Heart	heart
11	chr4:15486600-15499800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:15487200-15498800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:15487400-15570400	Weak transcription	Psoas Muscle	Psoas
14	chr4:15488800-15492200	ZNF genes & repeats	Fetal Lung	lung
15	chr4:15489800-15493000	Strong transcription	Stomach Smooth Muscle	stomach
16	chr4:15490200-15494200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:15490200-15498400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:15490400-15492000	Weak transcription	Pancreas	Pancrea
19	chr4:15490400-15498800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:15490400-15519400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:15490400-15539600	Weak transcription	Esophagus	oesophagus
22	chr4:15490600-15492400	Enhancers	Hela-S3	cervix
23	chr4:15490600-15492600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:15490600-15492600	Weak transcription	Left Ventricle	heart
25	chr4:15490600-15495000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr4:15490600-15497000	Weak transcription	Brain Substantia Nigra	brain
27	chr4:15490600-15497600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:15490600-15502400	Weak transcription	Lung	lung
29	chr4:15490600-15505000	Weak transcription	Adipose Nuclei	Adipose
30	chr4:15490600-15505200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:15490600-15510600	Weak transcription	Aorta	Aorta
32	chr4:15490600-15519000	Weak transcription	A549	lung
33	chr4:15490800-15493400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:15490800-15495800	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:15490800-15498200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr4:15490800-15504600	Weak transcription	Fetal Kidney	kidney
37	chr4:15491000-15492000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr4:15491000-15492400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:15491000-15492400	Weak transcription	Fetal Intestine Small	intestine
40	chr4:15491000-15495800	Weak transcription	Fetal Muscle Leg	muscle
41	chr4:15491000-15504400	Weak transcription	Fetal Intestine Large	intestine
42	chr4:15491200-15492400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr4:15491200-15504800	Weak transcription	Osteobl	bone
44	chr4:15491600-15492200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:15491600-15492400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:15491600-15494000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:15491600-15498400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr4:15491600-15498800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:15491600-15502400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:15491600-15504400	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links