Variant report

Variant	rs4942984
Chromosome Location	chr13:51818941-51818942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:51818423..51819959-chr13:51823241..51825450,2	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1108957	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1108958	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12584566	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs2408302	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3990078	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4942982	0.81[ASW][hapmap]

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	nsv832610	chr13:51636661-51822106	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832611	chr13:51766472-51938314	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4942984	VPS36	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51805200-51825600	Weak transcription	Aorta	Aorta
2	chr13:51808000-51821200	Enhancers	Brain Substantia Nigra	brain
3	chr13:51808400-51821400	Enhancers	Fetal Heart	heart
4	chr13:51808600-51820000	Weak transcription	Fetal Brain Female	brain
5	chr13:51810200-51820200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr13:51810400-51820000	Weak transcription	Fetal Brain Male	brain
7	chr13:51812600-51820600	Weak transcription	Right Ventricle	heart
8	chr13:51812600-51821000	Weak transcription	Spleen	Spleen
9	chr13:51813200-51822600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr13:51813600-51821200	Enhancers	Brain Cingulate Gyrus	brain
11	chr13:51814000-51819000	Enhancers	Colon Smooth Muscle	Colon
12	chr13:51814000-51820600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr13:51814200-51820200	Enhancers	Brain Anterior Caudate	brain
14	chr13:51814400-51819000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr13:51815000-51821400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr13:51815600-51821000	Weak transcription	Right Atrium	heart
17	chr13:51816200-51819000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr13:51816200-51820600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr13:51816200-51836600	Weak transcription	Adipose Nuclei	Adipose
20	chr13:51816400-51819200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr13:51816400-51820200	Enhancers	H1 Cell Line	embryonic stem cell
22	chr13:51816800-51820200	Weak transcription	Fetal Lung	lung
23	chr13:51816800-51836000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr13:51817000-51821000	Enhancers	Brain Angular Gyrus	brain
25	chr13:51817200-51819200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr13:51817400-51821200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr13:51817400-51827200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr13:51817600-51819200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr13:51817600-51819200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr13:51817600-51827200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr13:51817800-51819000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr13:51817800-51827600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr13:51818000-51819000	Genic enhancers	Brain Hippocampus Middle	brain
34	chr13:51818000-51819000	Enhancers	Left Ventricle	heart
35	chr13:51818000-51819200	Genic enhancers	Brain Inferior Temporal Lobe	brain
36	chr13:51818000-51819600	Genic enhancers	Stomach Smooth Muscle	stomach
37	chr13:51818000-51821200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr13:51818200-51819000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr13:51818200-51819200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr13:51818200-51819200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr13:51818200-51819600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr13:51818200-51820200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr13:51818200-51820200	Enhancers	Brain Germinal Matrix	brain
44	chr13:51818400-51819400	Weak transcription	Fetal Stomach	stomach
45	chr13:51818400-51820600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr13:51818600-51819000	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr13:51818600-51820200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr13:51818800-51819000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
49	chr13:51818800-51819000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
50	chr13:51818800-51820200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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