Variant report

Variant	rs2841548
Chromosome Location	chr6:13490584-13490585
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr6:13490574-13490643	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:13483604..13490047-chr6:13490051..13499001,13	K562	blood:
2	chr6:13489525..13492132-chr6:13508702..13511366,2	MCF-7	breast:
3	chr6:13484664..13490672-chr6:13572714..13577234,9	K562	blood:
4	chr6:13413198..13414739-chr6:13489299..13490913,2	MCF-7	breast:
5	chr6:13487471..13489124-chr6:13489749..13491815,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000187461	TF binding region
GFOD1	TF binding region
ENSG00000124523	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000187461	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11759779	0.92[ASN][1000 genomes]
rs2115063	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs2560761	0.84[CHB][hapmap]
rs2560789	0.85[CEU][hapmap];0.93[GIH][hapmap]
rs2560790	0.85[CEU][hapmap];0.93[GIH][hapmap]
rs2841549	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715379	0.85[CEU][hapmap]
rs6458872	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458898	0.85[CEU][hapmap]
rs7758810	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9367502	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9370156	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382154	0.92[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9382156	0.80[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1033620	chr6:13419730-13571788	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv462640	chr6:13426539-13519434	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv600994	chr6:13426539-13519434	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv470802	chr6:13441424-13519371	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2841548	GFOD1	cis	cerebellum	SCAN
rs2841548	C6orf52	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13488400-13494400	Weak transcription	HSMMtube	muscle
2	chr6:13489000-13490800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr6:13489000-13494200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:13489200-13490600	Weak transcription	Placenta	Placenta
5	chr6:13489200-13496600	Weak transcription	Spleen	Spleen
6	chr6:13489200-13496600	Weak transcription	GM12878-XiMat	blood
7	chr6:13489400-13493800	Weak transcription	Adipose Nuclei	Adipose
8	chr6:13489400-13494000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:13489400-13494200	Weak transcription	Fetal Heart	heart
10	chr6:13489400-13495600	Weak transcription	Left Ventricle	heart
11	chr6:13489600-13491600	Weak transcription	Esophagus	oesophagus
12	chr6:13489600-13493800	Weak transcription	Right Atrium	heart
13	chr6:13489600-13495600	Weak transcription	Right Ventricle	heart
14	chr6:13490400-13490600	Enhancers	NHDF-Ad	bronchial

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