Variant report

Variant	rs7253187
Chromosome Location	chr19:39465161-39465162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39450542..39452655-chr19:39464406..39466018,2	MCF-7	breast:
2	chr19:39341802..39343679-chr19:39464849..39468129,3	K562	blood:
3	chr19:39464164..39468178-chr19:39520932..39524285,4	MCF-7	breast:
4	chr19:39464957..39467280-chr19:39522120..39523795,2	K562	blood:

Variant related genes	Relation type
ENSG00000104824	Chromatin interaction
ENSG00000161243	Chromatin interaction
ENSG00000267992	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10412049	0.87[CEU][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs11083491	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12977030	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12982592	0.83[EUR][1000 genomes]
rs4803134	0.89[ASN][1000 genomes]
rs672685	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7253187	PVR	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39441200-39465200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr19:39441200-39465200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:39441200-39465200	Weak transcription	NHLF	lung
4	chr19:39441200-39465400	Weak transcription	Right Atrium	heart
5	chr19:39450000-39465400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:39453200-39465200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:39453200-39465200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr19:39453200-39465200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr19:39453200-39465200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr19:39453200-39465800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:39453200-39465800	Weak transcription	Pancreas	Pancrea
12	chr19:39453400-39465200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:39453400-39465200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:39453400-39465200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:39453400-39465200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:39453400-39465200	Weak transcription	Aorta	Aorta
17	chr19:39453400-39465200	Weak transcription	Brain Angular Gyrus	brain
18	chr19:39453400-39465200	Weak transcription	HSMM	muscle
19	chr19:39453400-39465200	Weak transcription	NH-A	brain
20	chr19:39453400-39465200	Weak transcription	NHEK	skin
21	chr19:39453400-39465400	Weak transcription	Brain Anterior Caudate	brain
22	chr19:39453400-39465400	Weak transcription	Brain Germinal Matrix	brain
23	chr19:39453400-39465400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr19:39456000-39465600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr19:39458800-39465200	Weak transcription	Colon Smooth Muscle	Colon
26	chr19:39458800-39465200	Weak transcription	Fetal Kidney	kidney
27	chr19:39459800-39465200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr19:39460000-39465200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:39460200-39465400	Weak transcription	Brain Substantia Nigra	brain
30	chr19:39460200-39465600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:39460800-39465200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr19:39461400-39465200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:39461400-39465200	Weak transcription	Adipose Nuclei	Adipose
34	chr19:39462200-39465200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr19:39462800-39465400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr19:39463800-39465200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:39464400-39465400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr19:39464600-39466800	Active TSS	HepG2	liver
39	chr19:39464800-39465200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:39464800-39465200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:39464800-39465200	Active TSS	A549	lung
42	chr19:39464800-39465400	Enhancers	Fetal Brain Male	brain
43	chr19:39464800-39465400	Active TSS	Osteobl	bone
44	chr19:39464800-39465600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:39465000-39465200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:39465000-39465200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:39465000-39465200	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr19:39465000-39465200	Active TSS	Muscle Satellite Cultured Cells	--
49	chr19:39465000-39465200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:39465000-39465200	Enhancers	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links