Variant report

Variant	rs6458849
Chromosome Location	chr6:13474277-13474278
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13474066..13476661-chr6:13573174..13576331,3	MCF-7	breast:
2	chr6:13461316..13464526-chr6:13474276..13478535,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124523	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2560812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2560814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58054832	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59330070	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62385807	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62385808	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6458848	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6906273	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	nsv520921	chr6:13474062-13479116	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6458849	RANBP9	cis	parietal	SCAN
rs6458849	C6orf114	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13452200-13483400	Weak transcription	Gastric	stomach
2	chr6:13454400-13485000	Weak transcription	Colonic Mucosa	Colon
3	chr6:13455200-13484400	Weak transcription	Small Intestine	intestine
4	chr6:13455200-13484600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:13455400-13481000	Weak transcription	HUVEC	blood vessel
6	chr6:13462800-13484800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:13463200-13481000	Weak transcription	A549	lung
8	chr6:13463400-13476600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:13463600-13484400	Weak transcription	Primary T cells from cord blood	blood
10	chr6:13463800-13484600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr6:13464600-13476400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:13465200-13485000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:13467000-13478600	Weak transcription	Thymus	Thymus
14	chr6:13467800-13474800	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:13468200-13474600	Weak transcription	Liver	Liver
16	chr6:13468200-13477000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:13469200-13480000	Weak transcription	Aorta	Aorta
18	chr6:13469400-13485800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:13470400-13474600	Enhancers	Right Ventricle	heart
20	chr6:13470600-13474800	Weak transcription	HMEC	breast
21	chr6:13470800-13474800	Enhancers	Spleen	Spleen
22	chr6:13470800-13477400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:13470800-13478800	Weak transcription	NHLF	lung
24	chr6:13470800-13480200	Weak transcription	NH-A	brain
25	chr6:13470800-13483600	Weak transcription	Fetal Stomach	stomach
26	chr6:13471000-13475600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:13471000-13485400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:13471000-13485600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:13471200-13474800	Weak transcription	Adipose Nuclei	Adipose
30	chr6:13471200-13478800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr6:13471200-13483400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr6:13471200-13483400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:13471400-13478600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:13471400-13478600	Weak transcription	Dnd41	blood
35	chr6:13471400-13480400	Weak transcription	Fetal Lung	lung
36	chr6:13471400-13484200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:13471600-13474800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr6:13471600-13477200	Weak transcription	Pancreas	Pancrea
39	chr6:13471600-13480200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr6:13471600-13481600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:13471600-13483600	Weak transcription	Fetal Muscle Leg	muscle
42	chr6:13471600-13485000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr6:13471800-13478800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr6:13471800-13480200	Weak transcription	Fetal Brain Male	brain
45	chr6:13471800-13485600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr6:13472000-13475200	Enhancers	K562	blood
47	chr6:13472000-13481800	Weak transcription	Brain Germinal Matrix	brain
48	chr6:13472200-13474800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr6:13472200-13484400	Weak transcription	Brain Substantia Nigra	brain
50	chr6:13472400-13481800	Weak transcription	Brain Anterior Caudate	brain

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