Variant report

Variant	rs7255983
Chromosome Location	chr19:18452759-18452760
allele	C/T
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18451193..18453522-chr19:18547468..18550080,2	K562	blood:
2	chr19:18263958..18265620-chr19:18450814..18453445,2	K562	blood:
3	chr19:18402536..18404490-chr19:18452623..18454131,2	MCF-7	breast:
4	chr19:18451491..18453396-chr19:18510638..18513266,2	K562	blood:
5	chr19:18448228..18453626-chr19:18495351..18501647,22	K562	blood:
6	chr19:18429634..18433959-chr19:18449815..18453704,5	K562	blood:
7	chr19:18448952..18453435-chr19:18523841..18530143,7	K562	blood:
8	chr19:18449115..18453939-chr19:18483257..18487784,7	K562	blood:
9	chr19:18334471..18336688-chr19:18451268..18453619,2	K562	blood:
10	chr19:18432103..18434677-chr19:18449671..18452769,4	MCF-7	breast:
11	chr19:18442556..18446502-chr19:18450638..18453378,4	MCF-7	breast:
12	chr19:18390145..18394362-chr19:18451018..18457221,11	MCF-7	breast:
13	chr19:18284581..18286574-chr19:18451473..18453390,2	K562	blood:
14	chr19:18388917..18393354-chr19:18447866..18453758,9	MCF-7	breast:
15	chr19:18441208..18448128-chr19:18448861..18453326,10	K562	blood:
16	chr19:18451842..18453468-chr19:18506301..18508301,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000105650	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000264175	Chromatin interaction
ENSG00000130520	Chromatin interaction
ENSG00000267959	Chromatin interaction
ENSG00000130511	Chromatin interaction
ENSG00000239821	Chromatin interaction
ENSG00000105655	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000216490	Chromatin interaction
ENSG00000268173	Chromatin interaction

Extended variants
information (count: 29 )
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]
rs10424419	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]
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:6 , 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	nsv911271	chr19:18362940-18453124	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7255983	PGPEP1	cis	Adipose Subcutaneous	GTEx
rs7255983	PGPEP1	cis	lung	GTEx
rs7255983	PGPEP1	cis	Nerve Tibial	GTEx
rs7255983	PGPEP1	cis	Esophagus Muscularis	GTEx
rs7255983	PGPEP1	cis	Artery Tibial	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18450600-18452800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:18450600-18452800	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr19:18450800-18452800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:18451000-18452800	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr19:18451400-18453600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr19:18452000-18452800	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr19:18452000-18454200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:18452200-18452800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr19:18452200-18452800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr19:18452200-18452800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr19:18452200-18452800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:18452200-18452800	Flanking Active TSS	Liver	Liver
13	chr19:18452200-18452800	Enhancers	Spleen	Spleen
14	chr19:18452200-18452800	Flanking Active TSS	GM12878-XiMat	blood
15	chr19:18452200-18452800	Flanking Active TSS	Hela-S3	cervix
16	chr19:18452200-18452800	Flanking Active TSS	HepG2	liver
17	chr19:18452200-18466200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr19:18452200-18466600	Weak transcription	Ovary	ovary
19	chr19:18452200-18468000	Weak transcription	Aorta	Aorta
20	chr19:18452400-18452800	Enhancers	H9 Cell Line	embryonic stem cell
21	chr19:18452400-18452800	Enhancers	Primary B cells from peripheral blood	blood
22	chr19:18452400-18452800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr19:18452400-18452800	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr19:18452400-18452800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr19:18452400-18452800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr19:18452400-18452800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr19:18452400-18452800	Enhancers	Brain Germinal Matrix	brain
28	chr19:18452400-18452800	Enhancers	Fetal Thymus	thymus
29	chr19:18452400-18452800	Enhancers	Pancreas	Pancrea
30	chr19:18452400-18452800	Transcr. at gene 5' and 3'	K562	blood
31	chr19:18452400-18453000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr19:18452400-18453000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr19:18452400-18453200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:18452400-18453200	Enhancers	Primary T cells fromperipheralblood	blood
35	chr19:18452400-18453400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr19:18452400-18453400	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr19:18452400-18453600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:18452400-18453600	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr19:18452400-18453600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
40	chr19:18452400-18453600	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr19:18452400-18453800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr19:18452400-18454400	Enhancers	Placenta	Placenta
43	chr19:18452400-18454600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:18452400-18455400	Weak transcription	Left Ventricle	heart
45	chr19:18452400-18457400	Enhancers	Stomach Mucosa	stomach
46	chr19:18452400-18460200	Weak transcription	Osteobl	bone
47	chr19:18452400-18466600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr19:18452400-18466600	Weak transcription	Right Ventricle	heart
49	chr19:18452400-18468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:18452400-18484800	Weak transcription	Right Atrium	heart

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