Variant report

Variant	rs56024260
Chromosome Location	chr20:13708796-13708797
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11696371	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026058	0.97[ASN][1000 genomes]
rs2031934	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088088	0.97[ASN][1000 genomes]
rs34414644	0.89[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	0.87[EUR][1000 genomes]
rs6079146	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079148	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079149	0.86[AFR][1000 genomes]
rs6079151	0.86[AFR][1000 genomes]
rs6079160	0.83[EUR][1000 genomes]
rs6079161	0.83[EUR][1000 genomes]
rs6079164	0.80[EUR][1000 genomes]
rs7273592	0.86[AFR][1000 genomes]
rs73094118	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73094125	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7353586	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56024260	NDUFAF5	cis	Esophagus Muscularis	GTEx
rs56024260	NDUFAF5	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13692200-13709200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr20:13692200-13712200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr20:13692200-13712400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:13692200-13745000	Weak transcription	Small Intestine	intestine
5	chr20:13692400-13712400	Weak transcription	Brain Germinal Matrix	brain
6	chr20:13692400-13717600	Strong transcription	Dnd41	blood
7	chr20:13692800-13712200	Weak transcription	Esophagus	oesophagus
8	chr20:13693000-13721400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr20:13693000-13746400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr20:13694400-13748000	Weak transcription	Gastric	stomach
11	chr20:13694600-13764400	Weak transcription	Stomach Mucosa	stomach
12	chr20:13694800-13718200	Weak transcription	Psoas Muscle	Psoas
13	chr20:13696000-13715600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr20:13697000-13712400	Weak transcription	Right Ventricle	heart
15	chr20:13697200-13711600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr20:13697200-13711800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr20:13697200-13711800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr20:13697200-13712400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr20:13697200-13712400	Weak transcription	Brain Angular Gyrus	brain
20	chr20:13697200-13712400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr20:13697200-13712400	Weak transcription	Brain Substantia Nigra	brain
22	chr20:13697200-13712600	Weak transcription	Colon Smooth Muscle	Colon
23	chr20:13697200-13745000	Weak transcription	Colonic Mucosa	Colon
24	chr20:13697400-13711600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr20:13697400-13712400	Weak transcription	NHEK	skin
26	chr20:13697600-13745800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr20:13698000-13709200	Weak transcription	Fetal Intestine Small	intestine
28	chr20:13698000-13712400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr20:13698200-13712400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr20:13698200-13712400	Weak transcription	Spleen	Spleen
31	chr20:13698200-13713000	Weak transcription	Brain Anterior Caudate	brain
32	chr20:13698400-13712200	Weak transcription	Thymus	Thymus
33	chr20:13698400-13739000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr20:13698600-13712200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr20:13698600-13725400	Weak transcription	Hela-S3	cervix
36	chr20:13699000-13712400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr20:13699200-13711600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr20:13699200-13712400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr20:13699400-13715600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr20:13699600-13712400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr20:13700400-13711400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr20:13700600-13710400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr20:13700800-13714400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr20:13700800-13728400	Weak transcription	Fetal Heart	heart
45	chr20:13702200-13712400	Weak transcription	Lung	lung
46	chr20:13702400-13717400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr20:13704000-13709200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr20:13704000-13710200	Strong transcription	HepG2	liver
49	chr20:13704200-13709200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr20:13704800-13710200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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