Variant report

Variant	rs2031934
Chromosome Location	chr20:13698885-13698886
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11696371	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026058	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs3088088	0.97[ASN][1000 genomes]
rs34414644	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56024260	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042314	0.85[ASN][1000 genomes]
rs6079143	0.97[ASN][1000 genomes]
rs6079144	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6079146	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079148	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079160	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6079161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6079164	0.80[EUR][1000 genomes]
rs6079174	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6079180	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs73094118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73094125	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73100123	0.82[AMR][1000 genomes]
rs7353586	0.86[AMR][1000 genomes];0.83[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2031934	NDUFAF5	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13690600-13706200	Weak transcription	Pancreas	Pancrea
2	chr20:13691800-13699000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr20:13691800-13706200	Weak transcription	Aorta	Aorta
4	chr20:13691800-13708000	Weak transcription	Fetal Brain Male	brain
5	chr20:13692200-13699800	Strong transcription	A549	lung
6	chr20:13692200-13709200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr20:13692200-13712200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr20:13692200-13712400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr20:13692200-13745000	Weak transcription	Small Intestine	intestine
10	chr20:13692400-13712400	Weak transcription	Brain Germinal Matrix	brain
11	chr20:13692400-13717600	Strong transcription	Dnd41	blood
12	chr20:13692600-13699200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr20:13692800-13699200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr20:13692800-13699600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr20:13692800-13699800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr20:13692800-13702200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr20:13692800-13702400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr20:13692800-13702600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr20:13692800-13712200	Weak transcription	Esophagus	oesophagus
20	chr20:13693000-13721400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr20:13693000-13746400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr20:13693400-13706800	Weak transcription	K562	blood
23	chr20:13693600-13699200	Strong transcription	Fetal Muscle Leg	muscle
24	chr20:13694000-13699200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr20:13694000-13699200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr20:13694000-13699200	Strong transcription	Duodenum Mucosa	Duodenum
27	chr20:13694200-13699000	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr20:13694200-13699600	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr20:13694200-13702400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr20:13694200-13702400	Strong transcription	HepG2	liver
31	chr20:13694200-13704200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr20:13694400-13699200	Strong transcription	Primary B cells from cord blood	blood
33	chr20:13694400-13699200	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr20:13694400-13699200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr20:13694400-13699200	Strong transcription	Fetal Thymus	thymus
36	chr20:13694400-13700000	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr20:13694400-13748000	Weak transcription	Gastric	stomach
38	chr20:13694600-13699200	Strong transcription	Primary B cells from peripheral blood	blood
39	chr20:13694600-13764400	Weak transcription	Stomach Mucosa	stomach
40	chr20:13694800-13718200	Weak transcription	Psoas Muscle	Psoas
41	chr20:13695000-13701800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr20:13695000-13708000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr20:13695400-13699800	Strong transcription	Primary hematopoietic stem cells	blood
44	chr20:13695400-13699800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr20:13695400-13702400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr20:13695600-13699200	Strong transcription	Primary T cells from cord blood	blood
47	chr20:13695800-13700400	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr20:13696000-13699000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr20:13696000-13699000	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr20:13696000-13699200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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