Variant report

Variant	rs10011930
Chromosome Location	chr4:125134554-125134555
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	chr4:125124930..125127393-chr4:125132171..125135021,2	MCF-7	breast:
2	chr4:125132533..125134622-chr4:125141190..125143971,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10021517	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11098744	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11732263	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11735374	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1357525	0.80[EUR][1000 genomes]
rs1370999	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1523494	0.85[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1523497	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1523498	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1583687	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1811417	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1829521	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2114041	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4109176	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4566664	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6534428	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6534434	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6834028	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6843899	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6847474	0.81[AMR][1000 genomes]
rs6857137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725001	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7657011	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7664885	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7671916	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7681352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7697184	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7697326	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs960925	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv868977	chr4:124841128-125550637	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv432624	chr4:125013395-125367740	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv998024	chr4:125019384-125380876	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv537241	chr4:125019384-125380876	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1015049	chr4:125037090-125393067	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10011930	NDUFAF2	trans	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:125133600-125134600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr4:125133600-125134800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:125133600-125134800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr4:125133600-125134800	Enhancers	Fetal Stomach	stomach
5	chr4:125133600-125134800	Enhancers	Hela-S3	cervix
6	chr4:125133600-125135000	Enhancers	Colon Smooth Muscle	Colon
7	chr4:125133800-125134600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:125133800-125134600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:125133800-125135000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:125134000-125134800	Enhancers	HSMMtube	muscle
11	chr4:125134000-125135000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:125134200-125134600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:125134400-125134800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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