Variant report

Variant	rs6079146
Chromosome Location	chr20:13695498-13695499
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:112678183..112678694-chr20:13694652..13695508,2	Hela-S3	cervix:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11696371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026058	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs2031934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088088	0.97[ASN][1000 genomes]
rs34414644	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56024260	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042314	0.85[ASN][1000 genomes]
rs6079143	0.97[ASN][1000 genomes]
rs6079144	0.90[EUR][1000 genomes]
rs6079148	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079149	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs6079151	0.96[AFR][1000 genomes]
rs6079160	0.88[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs6079161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs6079174	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6079180	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7273592	0.96[AFR][1000 genomes]
rs73094118	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73094125	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7353586	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1061323	chr20:13551004-13746346	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	esv1793063	chr20:13691562-13708788	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6079146	NDUFAF5	cis	Thyroid	GTEx
rs6079146	NDUFAF5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13690200-13696400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr20:13690400-13697000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr20:13690600-13695600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr20:13690600-13706200	Weak transcription	Pancreas	Pancrea
5	chr20:13691400-13696000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr20:13691400-13696200	Weak transcription	Right Ventricle	heart
7	chr20:13691600-13696000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr20:13691800-13699000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr20:13691800-13706200	Weak transcription	Aorta	Aorta
10	chr20:13691800-13708000	Weak transcription	Fetal Brain Male	brain
11	chr20:13692000-13696000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr20:13692200-13695600	Weak transcription	Thymus	Thymus
13	chr20:13692200-13696000	Weak transcription	Brain Angular Gyrus	brain
14	chr20:13692200-13696000	Weak transcription	Lung	lung
15	chr20:13692200-13696000	Weak transcription	Ovary	ovary
16	chr20:13692200-13696000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr20:13692200-13696200	Weak transcription	Brain Anterior Caudate	brain
18	chr20:13692200-13696800	Weak transcription	Spleen	Spleen
19	chr20:13692200-13698800	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr20:13692200-13699800	Strong transcription	A549	lung
21	chr20:13692200-13709200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr20:13692200-13712200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr20:13692200-13712400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr20:13692200-13745000	Weak transcription	Small Intestine	intestine
25	chr20:13692400-13696000	Weak transcription	Fetal Brain Female	brain
26	chr20:13692400-13696000	Weak transcription	HSMMtube	muscle
27	chr20:13692400-13698600	Strong transcription	Fetal Muscle Trunk	muscle
28	chr20:13692400-13712400	Weak transcription	Brain Germinal Matrix	brain
29	chr20:13692400-13717600	Strong transcription	Dnd41	blood
30	chr20:13692600-13696800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr20:13692600-13697400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr20:13692600-13698000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr20:13692600-13699200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr20:13692800-13695600	Weak transcription	NHEK	skin
35	chr20:13692800-13696200	Weak transcription	Colonic Mucosa	Colon
36	chr20:13692800-13696600	Weak transcription	HMEC	breast
37	chr20:13692800-13698200	Strong transcription	Adipose Nuclei	Adipose
38	chr20:13692800-13698400	Strong transcription	Liver	Liver
39	chr20:13692800-13698400	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr20:13692800-13699200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr20:13692800-13699600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr20:13692800-13699800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr20:13692800-13702200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr20:13692800-13702400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr20:13692800-13702600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr20:13692800-13712200	Weak transcription	Esophagus	oesophagus
47	chr20:13693000-13696000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr20:13693000-13721400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr20:13693000-13746400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr20:13693200-13696000	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links