Variant report

Variant	rs10424419
Chromosome Location	chr19:18453471-18453472
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	chr19:18451193..18453522-chr19:18547468..18550080,2	K562	blood:
2	chr19:18402536..18404490-chr19:18452623..18454131,2	MCF-7	breast:
3	chr19:18448228..18453626-chr19:18495351..18501647,22	K562	blood:
4	chr19:18429634..18433959-chr19:18449815..18453704,5	K562	blood:
5	chr19:18449115..18453939-chr19:18483257..18487784,7	K562	blood:
6	chr19:18334471..18336688-chr19:18451268..18453619,2	K562	blood:
7	chr19:18390145..18394362-chr19:18451018..18457221,11	MCF-7	breast:
8	chr19:18388917..18393354-chr19:18447866..18453758,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000264175	Chromatin interaction
ENSG00000130520	Chromatin interaction
ENSG00000105650	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000267959	Chromatin interaction
ENSG00000105655	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10401774	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10403547	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415319	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415765	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421763	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11881039	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882198	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978423	1.00[ASN][1000 genomes]
rs28503677	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55887446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56104914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56326450	1.00[ASN][1000 genomes]
rs6512259	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66732430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67348050	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251555	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253758	1.00[ASN][1000 genomes]
rs7255983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73009442	1.00[ASN][1000 genomes]
rs8102478	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102906	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112644	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
3	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
4	nsv911273	chr19:18386798-18454825	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	134 gene(s)	inside rSNPs	diseases
5	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10424419	PGPEP1	cis	Artery Tibial	GTEx
rs10424419	PGPEP1	cis	Nerve Tibial	GTEx
rs10424419	PGPEP1	cis	Adipose Subcutaneous	GTEx
rs10424419	PGPEP1	cis	lung	GTEx
rs10424419	PGPEP1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18451400-18453600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:18452000-18454200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:18452200-18466200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr19:18452200-18466600	Weak transcription	Ovary	ovary
5	chr19:18452200-18468000	Weak transcription	Aorta	Aorta
6	chr19:18452400-18453600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:18452400-18453600	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr19:18452400-18453600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
9	chr19:18452400-18453600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr19:18452400-18453800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:18452400-18454400	Enhancers	Placenta	Placenta
12	chr19:18452400-18454600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:18452400-18455400	Weak transcription	Left Ventricle	heart
14	chr19:18452400-18457400	Enhancers	Stomach Mucosa	stomach
15	chr19:18452400-18460200	Weak transcription	Osteobl	bone
16	chr19:18452400-18466600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:18452400-18466600	Weak transcription	Right Ventricle	heart
18	chr19:18452400-18468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:18452400-18484800	Weak transcription	Right Atrium	heart
20	chr19:18452600-18453600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
21	chr19:18452600-18454000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr19:18452600-18454200	Weak transcription	HMEC	breast
23	chr19:18452600-18454200	Weak transcription	NHEK	skin
24	chr19:18452600-18454800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:18452600-18454800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr19:18452600-18454800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:18452600-18454800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr19:18452600-18455000	Weak transcription	NH-A	brain
29	chr19:18452600-18455200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr19:18452600-18455200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr19:18452600-18455200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr19:18452600-18455600	Genic enhancers	Rectal Mucosa Donor 29	rectum
33	chr19:18452600-18455600	Weak transcription	A549	lung
34	chr19:18452600-18455800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:18452600-18456000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr19:18452600-18456400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr19:18452600-18456800	Weak transcription	Primary T cells from cord blood	blood
38	chr19:18452600-18456800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:18452600-18458800	Weak transcription	Fetal Brain Male	brain
40	chr19:18452600-18461200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr19:18452600-18464000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr19:18452600-18466400	Weak transcription	Brain Angular Gyrus	brain
43	chr19:18452600-18466400	Weak transcription	Colon Smooth Muscle	Colon
44	chr19:18452600-18466400	Weak transcription	Fetal Lung	lung
45	chr19:18452600-18466400	Weak transcription	HSMMtube	muscle
46	chr19:18452600-18466600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:18452600-18466600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:18452600-18466600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr19:18452600-18466600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr19:18452600-18466600	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links