Variant report

Variant	rs3912916
Chromosome Location	chr4:95420477-95420478
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95420294..95421871-chr4:95428867..95430685,2	K562	blood:

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10019354	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020710	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774992	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs902980	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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
rs3912916	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 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	chr4:95387400-95420800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:95394400-95428000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:95398400-95428400	Weak transcription	Small Intestine	intestine
5	chr4:95400800-95440000	Weak transcription	Lung	lung
6	chr4:95401800-95420800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:95405000-95429000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:95407200-95428000	Weak transcription	Placenta	Placenta
9	chr4:95408000-95428000	Weak transcription	K562	blood
10	chr4:95408200-95422000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:95409000-95422000	Weak transcription	Ovary	ovary
12	chr4:95410200-95422000	Weak transcription	Right Atrium	heart
13	chr4:95411000-95427800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:95412400-95422000	Weak transcription	Liver	Liver
15	chr4:95412400-95424600	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:95412800-95426000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:95412800-95428400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:95413000-95426200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:95413200-95427400	Weak transcription	A549	lung
20	chr4:95413200-95428000	Weak transcription	Hela-S3	cervix
21	chr4:95413400-95425800	Weak transcription	HSMMtube	muscle
22	chr4:95413400-95428000	Weak transcription	NH-A	brain
23	chr4:95413400-95428400	Weak transcription	NHLF	lung
24	chr4:95413600-95421800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:95413600-95425600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:95414600-95429000	Weak transcription	Esophagus	oesophagus
27	chr4:95415400-95420800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:95415400-95420800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:95415400-95425800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:95415400-95429000	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:95415400-95440200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:95416000-95421000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr4:95416200-95427400	Weak transcription	Fetal Intestine Large	intestine
34	chr4:95416400-95425600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:95417000-95420800	Weak transcription	Fetal Intestine Small	intestine
36	chr4:95417000-95420800	Weak transcription	Left Ventricle	heart
37	chr4:95417000-95427200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr4:95417200-95426800	Weak transcription	HUVEC	blood vessel
39	chr4:95417200-95428000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr4:95417600-95422400	Weak transcription	Osteobl	bone
41	chr4:95418000-95420800	Weak transcription	Psoas Muscle	Psoas
42	chr4:95418000-95425800	Weak transcription	Right Ventricle	heart
43	chr4:95418000-95430800	Weak transcription	Pancreas	Pancrea
44	chr4:95418200-95420800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:95418400-95420600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr4:95419000-95421600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:95419200-95420600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr4:95419600-95428400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:95419800-95421600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:95419800-95427800	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links