Variant report

Variant	rs13120717
Chromosome Location	chr4:53846584-53846585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53583775..53586079-chr4:53843904..53846778,2	MCF-7	breast:
2	chr4:53581143..53582877-chr4:53845508..53847692,2	K562	blood:
3	chr4:53524811..53526481-chr4:53845807..53848111,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248866	Chromatin interaction
ENSG00000109189	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10010254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133240	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13104612	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13104971	1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes]
rs13123449	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13134756	0.89[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1319626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1384695	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1531836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2170689	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898683	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs301089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs301110	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs301112	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34704735	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3849652	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs403536	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6554062	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554063	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831230	0.93[EUR][1000 genomes]
rs6844522	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6853639	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7685087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689426	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs958693	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv508280	chr4:53825060-53907661	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13120717	NMU	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53786600-53861400	Weak transcription	Primary B cells from cord blood	blood
2	chr4:53818200-53849800	Weak transcription	Primary T cells from cord blood	blood
3	chr4:53838800-53850200	Weak transcription	Aorta	Aorta
4	chr4:53842800-53848400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:53843200-53847800	Weak transcription	Fetal Heart	heart
6	chr4:53844000-53848000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:53844400-53847400	Weak transcription	Fetal Kidney	kidney
8	chr4:53844400-53849200	Weak transcription	Fetal Stomach	stomach
9	chr4:53844400-53850000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:53844400-53850200	Weak transcription	Ovary	ovary
11	chr4:53844600-53847800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:53844600-53848000	Weak transcription	Fetal Brain Female	brain
13	chr4:53844600-53848400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr4:53844600-53848400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:53844600-53850000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:53844600-53850000	Weak transcription	Colon Smooth Muscle	Colon
17	chr4:53845200-53847000	Weak transcription	Placenta	Placenta
18	chr4:53846000-53846800	Enhancers	HMEC	breast
19	chr4:53846000-53846800	Enhancers	NHEK	skin
20	chr4:53846200-53848200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr4:53846200-53850000	Weak transcription	Rectal Mucosa Donor 31	rectum

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