Variant report

Variant	rs253072
Chromosome Location	chr5:76024819-76024820
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	chr5:76023117..76024949-chr5:76027820..76030063,2	K562	blood:
2	chr5:76023449..76027739-chr5:76027820..76030075,3	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs152778	0.83[ASN][1000 genomes]
rs153310	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs193943	0.84[ASN][1000 genomes]
rs250716	0.84[ASN][1000 genomes]
rs250717	0.85[ASN][1000 genomes]
rs250719	0.85[ASN][1000 genomes]
rs250730	0.94[ASN][1000 genomes]
rs250731	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs250739	0.87[ASN][1000 genomes]
rs250741	0.88[ASN][1000 genomes]
rs250742	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs250744	0.88[ASN][1000 genomes]
rs250745	0.88[ASN][1000 genomes]
rs250746	0.88[ASN][1000 genomes]
rs250747	0.87[ASN][1000 genomes]
rs250748	0.88[ASN][1000 genomes]
rs250750	0.88[ASN][1000 genomes]
rs250751	0.88[ASN][1000 genomes]
rs250752	0.88[ASN][1000 genomes]
rs253073	1.00[ASN][1000 genomes]
rs37250	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs705402	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1035135	chr5:75927027-76092058	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv882207	chr5:75997213-76027823	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv882208	chr5:75997213-76034355	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv882209	chr5:76004933-76034355	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs253072	F2R	cis	lung	GTEx
rs253072	F2R	cis	Muscle Skeletal	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:76013000-76028400	Weak transcription	Aorta	Aorta
2	chr5:76013000-76032000	Weak transcription	HSMM	muscle
3	chr5:76013000-76033000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:76013800-76028400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:76013800-76030800	Weak transcription	Ovary	ovary
6	chr5:76014000-76028400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:76014400-76025400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:76014400-76025400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr5:76017000-76028400	Weak transcription	Spleen	Spleen
10	chr5:76018400-76034400	Weak transcription	Left Ventricle	heart
11	chr5:76018600-76025600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:76021000-76025200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:76021000-76025200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:76021000-76026400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:76021000-76030400	Strong transcription	HUVEC	blood vessel
16	chr5:76021200-76027000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:76021200-76034200	Weak transcription	HepG2	liver
18	chr5:76021400-76025000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:76021400-76025200	Weak transcription	NHDF-Ad	bronchial
20	chr5:76021400-76025400	Weak transcription	K562	blood
21	chr5:76021400-76025400	Weak transcription	Osteobl	bone
22	chr5:76021800-76026000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:76022000-76030600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:76022400-76026200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:76022400-76026600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:76022400-76027000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr5:76022600-76026600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:76022600-76026600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
29	chr5:76022800-76026600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:76022800-76026600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
31	chr5:76022800-76027000	ZNF genes & repeats	Fetal Lung	lung
32	chr5:76023000-76026600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:76023000-76030400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:76023200-76025400	Weak transcription	Fetal Brain Male	brain
35	chr5:76023400-76025200	Strong transcription	NHLF	lung
36	chr5:76023400-76025400	Weak transcription	NH-A	brain
37	chr5:76024000-76026600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
38	chr5:76024200-76025600	ZNF genes & repeats	Fetal Kidney	kidney
39	chr5:76024200-76026200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:76024200-76027000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:76024200-76027000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
42	chr5:76024400-76025400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:76024600-76025000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr5:76024600-76025200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr5:76024600-76027000	ZNF genes & repeats	Fetal Brain Female	brain
46	chr5:76024800-76025400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr5:76024800-76025600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:76024800-76026200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
49	chr5:76024800-76026200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links