Variant report

Variant	rs338583
Chromosome Location	chr19:41712424-41712425
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41711572..41712536-chr19:41767839..41768829,4	MCF-7	breast:
2	chr19:41711877..41715272-chr19:41724756..41728311,4	K562	blood:
3	chr19:41710873..41712522-chr19:41830997..41833166,2	K562	blood:
4	chr19:41710998..41712626-chr19:41765390..41767317,2	K562	blood:
5	chr19:41710579..41716236-chr19:41767651..41773158,11	K562	blood:
6	chr19:41709626..41713446-chr19:41767553..41770209,4	MCF-7	breast:
7	chr19:41711943..41714623-chr19:41813301..41815470,3	MCF-7	breast:
8	chr19:41711670..41712535-chr19:41768074..41768746,2	MCF-7	breast:
9	chr19:41708734..41715779-chr19:41765259..41771124,12	K562	blood:
10	chr19:41712333..41715272-chr19:41724873..41727536,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000167601	Chromatin interaction
ENSG00000269652	Chromatin interaction
ENSG00000105323	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12984631	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1623906	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1709104	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1709139	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs338584	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs338596	0.83[JPT][hapmap]
rs8101985	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8192798	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911767	chr19:41649516-41716271	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv911768	chr19:41680424-41748753	Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs338583	PNKP	cis	parietal	SCAN
rs338583	PSG8	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41699600-41724400	Weak transcription	Right Atrium	heart
2	chr19:41700000-41722200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr19:41700000-41724400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:41700200-41724200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:41700600-41714600	Weak transcription	Spleen	Spleen
6	chr19:41701200-41713800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr19:41701600-41713800	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr19:41701600-41714600	Strong transcription	Fetal Intestine Small	intestine
9	chr19:41701800-41714400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr19:41701800-41714800	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr19:41702000-41713800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:41702000-41722400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr19:41702200-41714000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr19:41702800-41713600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:41702800-41713800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
16	chr19:41703000-41714600	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr19:41705400-41713200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr19:41706400-41713800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr19:41707000-41713800	Strong transcription	Fetal Intestine Large	intestine
20	chr19:41707800-41723600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr19:41708400-41712800	Weak transcription	Small Intestine	intestine
22	chr19:41710200-41716800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:41710400-41722400	Weak transcription	HepG2	liver
24	chr19:41710600-41713000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
25	chr19:41710800-41713600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr19:41711000-41712800	Weak transcription	Right Ventricle	heart
27	chr19:41711000-41713400	Strong transcription	Fetal Stomach	stomach
28	chr19:41711000-41713800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr19:41711200-41713600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr19:41711400-41713000	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr19:41711400-41713400	Strong transcription	Esophagus	oesophagus
32	chr19:41711400-41713800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:41711400-41713800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:41711600-41712800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr19:41711600-41713000	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr19:41711600-41713600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:41711600-41713600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:41711800-41712800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:41711800-41712800	Genic enhancers	A549	lung
40	chr19:41711800-41713000	Strong transcription	Lung	lung
41	chr19:41711800-41713200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr19:41711800-41713400	Genic enhancers	Stomach Mucosa	stomach
43	chr19:41711800-41713400	Strong transcription	NHEK	skin
44	chr19:41711800-41713800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:41711800-41713800	Enhancers	HSMM	muscle
46	chr19:41712000-41712800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:41712000-41712800	Strong transcription	Colonic Mucosa	Colon
48	chr19:41712000-41712800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
49	chr19:41712000-41713200	Enhancers	K562	blood
50	chr19:41712000-41713200	Enhancers	NHDF-Ad	bronchial

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