Variant report

Variant	rs4952916
Chromosome Location	chr2:48769377-48769378
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	chr2:48767423..48771041-chr2:48771579..48775293,4	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11689512	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11694952	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11695393	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72822289	0.96[EUR][1000 genomes]
rs72822291	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7557600	0.93[EUR][1000 genomes]
rs7587917	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1007491	chr2:48752185-48796441	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv535683	chr2:48752185-48796441	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv581776	chr2:48763382-48913019	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1000419	chr2:48766957-48795327	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4952916	FOXN2	cis	parietal	SCAN
rs4952916	STON1-GTF2A1L	cis	cerebellum	SCAN
rs4952916	PPP1R21	cis	Thyroid	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48758800-48772400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:48759000-48772600	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:48759000-48775200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:48759000-48787000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr2:48759000-48787400	Weak transcription	Psoas Muscle	Psoas
6	chr2:48759000-48827600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:48759200-48793200	Weak transcription	Fetal Lung	lung
8	chr2:48759400-48775200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:48760000-48770800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:48760000-48771000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:48760000-48772000	Weak transcription	Lung	lung
12	chr2:48760000-48772400	Weak transcription	Right Atrium	heart
13	chr2:48760400-48772800	Weak transcription	Left Ventricle	heart
14	chr2:48762600-48775000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:48766800-48779600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:48767200-48772600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:48767200-48807800	Weak transcription	Aorta	Aorta
18	chr2:48767400-48775200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:48767600-48772400	Weak transcription	K562	blood
20	chr2:48767800-48769800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:48767800-48771000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:48767800-48772600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:48767800-48776400	Weak transcription	Fetal Stomach	stomach
24	chr2:48768000-48770800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:48768000-48772000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:48768000-48772400	Weak transcription	Placenta	Placenta
27	chr2:48768000-48787600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:48768000-48793800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:48768200-48772400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr2:48768600-48777000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:48769000-48769400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:48769000-48769400	Enhancers	Colon Smooth Muscle	Colon
33	chr2:48769000-48769400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr2:48769000-48769400	Enhancers	Placenta Amnion	Placenta Amnion
35	chr2:48769000-48769400	Enhancers	Stomach Smooth Muscle	stomach
36	chr2:48769000-48769600	Enhancers	Ovary	ovary
37	chr2:48769000-48776000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:48769200-48769400	Enhancers	Fetal Heart	heart
39	chr2:48769200-48771400	Weak transcription	NHDF-Ad	bronchial

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