Variant report

Variant	rs4953572
Chromosome Location	chr2:48624007-48624008
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	chr2:48617829..48620871-chr2:48622412..48626412,3	K562	blood:
2	chr2:48130775..48133582-chr2:48622856..48624453,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233230	Chromatin interaction
ENSG00000138081	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10169629	0.94[EUR][1000 genomes]
rs11680719	0.90[EUR][1000 genomes]
rs11683099	0.96[EUR][1000 genomes]
rs11689645	0.90[EUR][1000 genomes]
rs12328506	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs13398791	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs17855177	0.95[CEU][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs4953579	0.86[JPT][hapmap]
rs55744465	0.85[EUR][1000 genomes]
rs56391806	0.85[EUR][1000 genomes]
rs6705802	0.91[CEU][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs6718068	0.95[CEU][hapmap];0.80[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs6722246	0.86[EUR][1000 genomes]
rs6745580	0.88[EUR][1000 genomes]
rs72820445	0.95[EUR][1000 genomes]
rs7566239	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs7569575	0.89[MEX][hapmap]
rs7573316	0.91[EUR][1000 genomes]
rs7576964	0.95[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs7577237	0.95[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap];0.95[EUR][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	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv518718	chr2:48624007-48650308	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4953572	TTC7A	cis	cerebellum	SCAN
rs4953572	STON1-GTF2A1L	cis	cerebellum	SCAN
rs4953572	PPP1R21	cis	Thyroid	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48619200-48624600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:48619400-48624600	Weak transcription	Brain Angular Gyrus	brain
3	chr2:48619400-48624600	Weak transcription	Brain Anterior Caudate	brain
4	chr2:48619400-48624600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:48619400-48625400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:48619600-48624400	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:48622800-48624200	Enhancers	Primary T cells from cord blood	blood
8	chr2:48623200-48624600	Weak transcription	Adipose Nuclei	Adipose
9	chr2:48623200-48625600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr2:48623400-48624800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:48623600-48624800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr2:48623600-48625400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr2:48623600-48626800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:48623600-48626800	Weak transcription	Fetal Intestine Large	intestine
15	chr2:48623600-48626800	Weak transcription	Fetal Intestine Small	intestine
16	chr2:48623800-48624600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:48623800-48626600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:48624000-48624200	Enhancers	Fetal Brain Male	brain
19	chr2:48624000-48624400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:48624000-48624600	Enhancers	Brain Germinal Matrix	brain
21	chr2:48624000-48624600	Enhancers	Fetal Brain Female	brain
22	chr2:48624000-48625000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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