Variant report

Variant	rs10000208
Chromosome Location	chr4:95467095-95467096
allele	A/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	chr4:95464708..95469426-chr4:95470140..95474023,5	K562	blood:
2	chr4:95382396..95384171-chr4:95466994..95469392,2	K562	blood:
3	chr4:95372608..95374440-chr4:95464990..95467964,2	MCF-7	breast:
4	chr4:95458379..95460078-chr4:95465243..95467289,2	K562	blood:
5	chr4:95460565..95462692-chr4:95465018..95467575,2	K562	blood:
6	chr4:95443443..95445921-chr4:95466329..95468317,2	K562	blood:
7	chr4:95466562..95469843-chr4:95470075..95473924,5	K562	blood:
8	chr4:95452128..95455123-chr4:95466156..95467700,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163110	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10025074	0.87[EUR][1000 genomes]
rs10213504	0.89[EUR][1000 genomes]
rs2510766	0.86[EUR][1000 genomes]
rs2510771	0.87[EUR][1000 genomes]
rs3792664	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805274	0.86[EUR][1000 genomes]
rs3805283	0.91[EUR][1000 genomes]
rs6812098	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6830074	0.86[EUR][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
rs10000208	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95422400-95482800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:95442000-95469600	Weak transcription	Primary T cells from cord blood	blood
3	chr4:95449200-95470200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:95456800-95469800	Weak transcription	Ovary	ovary
5	chr4:95456800-95470200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:95457000-95469800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:95457400-95469800	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:95457400-95470000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:95457400-95485400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:95458000-95469800	Weak transcription	Small Intestine	intestine
11	chr4:95458000-95480400	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:95458200-95483000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:95458200-95488800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr4:95458400-95468600	Weak transcription	Liver	Liver
15	chr4:95458400-95469800	Weak transcription	Fetal Intestine Large	intestine
16	chr4:95459000-95473000	Weak transcription	Fetal Kidney	kidney
17	chr4:95459000-95480400	Weak transcription	Adipose Nuclei	Adipose
18	chr4:95459600-95471000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:95459800-95481200	Weak transcription	Aorta	Aorta
20	chr4:95460200-95472400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:95460400-95469800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:95462200-95468400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr4:95462600-95470200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:95463000-95468400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:95463000-95469600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:95463000-95469600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:95463000-95480400	Weak transcription	Right Ventricle	heart
28	chr4:95463000-95487800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:95463200-95470000	Weak transcription	Fetal Intestine Small	intestine
30	chr4:95463200-95481200	Weak transcription	Left Ventricle	heart
31	chr4:95464800-95467600	Enhancers	Fetal Heart	heart
32	chr4:95465000-95467600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:95465200-95467200	Enhancers	NHEK	skin
34	chr4:95465200-95467400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:95465200-95467400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:95465200-95469200	Enhancers	Muscle Satellite Cultured Cells	--
37	chr4:95465600-95467600	Enhancers	HSMMtube	muscle
38	chr4:95465600-95467600	Enhancers	Osteobl	bone
39	chr4:95465600-95467800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr4:95465800-95467200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:95466000-95467200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:95466000-95470000	Weak transcription	Placenta	Placenta
43	chr4:95466000-95474800	Weak transcription	Psoas Muscle	Psoas
44	chr4:95466000-95475000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr4:95466200-95467400	Enhancers	HSMM	muscle
46	chr4:95466200-95467400	Enhancers	NH-A	brain
47	chr4:95466400-95467600	Enhancers	Rectal Smooth Muscle	rectum
48	chr4:95466600-95467400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:95466600-95467600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:95466600-95467600	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links