Variant report

Variant	rs2059804
Chromosome Location	chr6:13489400-13489401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr6:13487982-13489417	H1-hESC	embryonic stem cell:	n/a	chr6:13488882-13488892 chr6:13488624-13488633 chr6:13488144-13488158 chr6:13488515-13488524

No.	Distal block	Cell Line	Cell type
1	chr6:13489026..13490564-chr6:13494155..13495687,2	K562	blood:
2	chr6:13484664..13490672-chr6:13572714..13577234,9	K562	blood:
3	chr6:13484393..13490113-chr6:13572102..13578017,14	MCF-7	breast:
4	chr6:13485388..13489511-chr6:13572660..13577514,13	MCF-7	breast:
5	chr6:13413198..13414739-chr6:13489299..13490913,2	MCF-7	breast:
6	chr6:13488196..13489716-chr6:13537164..13538771,2	MCF-7	breast:
7	chr6:13486736..13489619-chr6:13614070..13616875,2	MCF-7	breast:

Variant related genes	Relation type
GFOD1	TF binding region
ENSG00000187461	TF binding region
ENSG00000261071	Chromatin interaction
ENSG00000225921	Chromatin interaction
ENSG00000124523	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1992387	0.82[JPT][hapmap]
rs7739372	1.00[JPT][hapmap]
rs9382141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382144	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs9382154	0.87[ASW][hapmap];0.87[YRI][hapmap]
rs9395813	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[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	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
6	esv3421701	chr6:13485573-13489871	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2059804	RNF182	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13485000-13489600	Active TSS	Rectal Smooth Muscle	rectum
2	chr6:13488200-13489400	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr6:13488400-13489400	Enhancers	Fetal Heart	heart
4	chr6:13488400-13494400	Weak transcription	HSMMtube	muscle
5	chr6:13488600-13489400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:13488600-13489400	Enhancers	Lung	lung
7	chr6:13488600-13490200	Weak transcription	NHDF-Ad	bronchial
8	chr6:13488800-13489400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:13488800-13489400	Flanking Active TSS	Brain Hippocampus Middle	brain
10	chr6:13488800-13489400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr6:13488800-13489400	Enhancers	Left Ventricle	heart
12	chr6:13488800-13489600	Enhancers	Right Ventricle	heart
13	chr6:13489000-13489400	Enhancers	Primary B cells from peripheral blood	blood
14	chr6:13489000-13489400	Enhancers	Brain Substantia Nigra	brain
15	chr6:13489000-13489600	Enhancers	Esophagus	oesophagus
16	chr6:13489000-13489600	Enhancers	Right Atrium	heart
17	chr6:13489000-13489600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr6:13489000-13490800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr6:13489000-13494200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:13489200-13489400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:13489200-13489400	Enhancers	Adipose Nuclei	Adipose
22	chr6:13489200-13489400	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr6:13489200-13489400	Flanking Bivalent TSS/Enh	HepG2	liver
24	chr6:13489200-13489600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr6:13489200-13490600	Weak transcription	Placenta	Placenta
26	chr6:13489200-13496600	Weak transcription	Spleen	Spleen
27	chr6:13489200-13496600	Weak transcription	GM12878-XiMat	blood
28	chr6:13489400-13489600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:13489400-13493800	Weak transcription	Adipose Nuclei	Adipose
30	chr6:13489400-13494000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:13489400-13494200	Weak transcription	Fetal Heart	heart
32	chr6:13489400-13495600	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links