Variant report

Variant	rs902980
Chromosome Location	chr4:95429441-95429442
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95429157..95431887-chr4:95434786..95438000,3	K562	blood:
2	chr4:95372282..95374578-chr4:95428337..95431259,2	K562	blood:
3	chr4:95372028..95373617-chr4:95427341..95430036,2	MCF-7	breast:
4	chr4:95420294..95421871-chr4:95428867..95430685,2	K562	blood:
5	chr4:95372296..95374586-chr4:95428181..95430528,2	MCF-7	breast:
6	chr4:95371846..95374578-chr4:95428736..95431275,4	K562	blood:

Variant related genes	Relation type
ENSG00000163110	Chromatin interaction
ENSG00000203436	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10019354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577055	0.86[CHD][hapmap];0.85[JPT][hapmap]
rs3912916	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs699861	0.82[CEU][hapmap]
rs7679284	0.88[CEU][hapmap]
rs774992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv594901	chr4:95254730-95493246	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1003743	chr4:95255957-95469831	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs902980	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95375000-95440200	Weak transcription	Primary T cells from cord blood	blood
2	chr4:95400800-95440000	Weak transcription	Lung	lung
3	chr4:95415400-95440200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr4:95418000-95430800	Weak transcription	Pancreas	Pancrea
5	chr4:95421200-95429600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:95421200-95440000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:95421400-95431400	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr4:95421600-95440000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:95422400-95482800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr4:95423200-95436600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:95424600-95431800	Enhancers	Colon Smooth Muscle	Colon
12	chr4:95425600-95429800	Enhancers	Psoas Muscle	Psoas
13	chr4:95427000-95430600	Enhancers	Liver	Liver
14	chr4:95427200-95429600	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr4:95427400-95430400	Enhancers	Fetal Intestine Large	intestine
16	chr4:95427600-95429800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:95427600-95430400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:95427800-95429600	Genic enhancers	NHEK	skin
19	chr4:95427800-95429800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:95427800-95430200	Enhancers	HepG2	liver
21	chr4:95427800-95430400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr4:95427800-95430400	Enhancers	HMEC	breast
23	chr4:95427800-95430600	Enhancers	Osteobl	bone
24	chr4:95427800-95431400	Enhancers	Duodenum Mucosa	Duodenum
25	chr4:95428000-95429800	Enhancers	Gastric	stomach
26	chr4:95428000-95429800	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr4:95428000-95430000	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr4:95428000-95430200	Enhancers	K562	blood
29	chr4:95428000-95430400	Enhancers	NH-A	brain
30	chr4:95428000-95430600	Enhancers	Hela-S3	cervix
31	chr4:95428000-95430800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr4:95428200-95429600	Weak transcription	Right Ventricle	heart
33	chr4:95428200-95429800	Enhancers	HUVEC	blood vessel
34	chr4:95428200-95430200	Enhancers	Stomach Mucosa	stomach
35	chr4:95428400-95430000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:95428400-95430000	Enhancers	Small Intestine	intestine
37	chr4:95428400-95430400	Enhancers	Fetal Intestine Small	intestine
38	chr4:95428400-95430400	Enhancers	NHDF-Ad	bronchial
39	chr4:95428400-95430600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr4:95428400-95430600	Enhancers	NHLF	lung
41	chr4:95428600-95429600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:95428600-95429800	Flanking Active TSS	A549	lung
43	chr4:95428600-95430400	Enhancers	Adipose Nuclei	Adipose
44	chr4:95428600-95430400	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr4:95428600-95430400	Enhancers	Fetal Lung	lung
46	chr4:95428600-95430800	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr4:95428800-95429800	Flanking Active TSS	Fetal Heart	heart
48	chr4:95428800-95429800	Enhancers	Right Atrium	heart
49	chr4:95428800-95430200	Enhancers	Brain Anterior Caudate	brain
50	chr4:95428800-95430400	Enhancers	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links