Variant report

Variant	rs6016973
Chromosome Location	chr20:41817077-41817078
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	CTCF	chr20:41816020-41817330	SK-N-SH	brain:	n/a	chr20:41816561-41816574 chr20:41816560-41816576 chr20:41816559-41816577 chr20:41816561-41816574
2	REST	chr20:41816127-41817149	HL-60	blood:	n/a	chr20:41816422-41816430 chr20:41816893-41816902 chr20:41817115-41817122
3	SIN3A	chr20:41816387-41817154	H1-hESC	embryonic stem cell:	n/a	n/a
4	REST	chr20:41816122-41817095	H1-neurons	neurons:	n/a	chr20:41816422-41816430 chr20:41816893-41816902
5	CTCF	chr20:41817020-41817170	HepG2	liver:	n/a	n/a
6	POLR2A	chr20:41816498-41817319	H1-neurons	neurons:	n/a	n/a
7	CTCF	chr20:41816940-41817090	BJ	skin:	n/a	n/a
8	SUZ12	chr20:41816560-41819205	NT2-D1	testis:	n/a	n/a
9	YY1	chr20:41816458-41817227	H1-hESC	embryonic stem cell:	n/a	chr20:41817021-41817031
10	RAD21	chr20:41816209-41817252	H1-hESC	embryonic stem cell:	n/a	chr20:41816557-41816576
11	RAD21	chr20:41815974-41817339	SK-N-SH	brain:	n/a	chr20:41816557-41816576 chr20:41817274-41817287
12	SMC3	chr20:41816128-41817262	SK-N-SH	brain:	n/a	chr20:41816561-41816571 chr20:41816561-41816575
13	POLR2A	chr20:41816483-41817382	H1-neurons	neurons:	n/a	n/a
14	CTCF	chr20:41816960-41817110	BJ	skin:	n/a	n/a

Variant related genes	Relation type
ENSG00000233508	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2425613	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2425615	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2425617	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2867655	0.80[ASN][1000 genomes]
rs4812690	0.82[ASN][1000 genomes]
rs6065588	0.93[ASN][1000 genomes]
rs61034448	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063450	chr20:41409901-41880620	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1060690	chr20:41413369-41851935	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1066088	chr20:41417205-42060036	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv2751914	chr20:41744586-41890453	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41815400-41819000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr20:41816400-41817200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
3	chr20:41816600-41817200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
4	chr20:41816600-41817200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
5	chr20:41816600-41817200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
6	chr20:41816600-41817200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
7	chr20:41816600-41817200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
8	chr20:41816600-41817200	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
9	chr20:41816600-41817200	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
10	chr20:41816600-41817400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
11	chr20:41816600-41817600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
12	chr20:41816600-41817800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr20:41816600-41817800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr20:41816600-41818000	Enhancers	Liver	Liver
15	chr20:41816600-41818200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
16	chr20:41816600-41818200	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
17	chr20:41816600-41818800	Active TSS	Aorta	Aorta
18	chr20:41816600-41819000	Enhancers	Pancreas	Pancrea
19	chr20:41816600-41819200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr20:41816600-41819400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
21	chr20:41816600-41819400	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr20:41816800-41817200	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
23	chr20:41816800-41817200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
24	chr20:41816800-41817200	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr20:41816800-41817200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr20:41816800-41817200	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
27	chr20:41816800-41817200	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
28	chr20:41816800-41817200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
29	chr20:41816800-41817200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr20:41816800-41817200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
31	chr20:41816800-41817200	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
32	chr20:41816800-41817200	Bivalent Enhancer	Left Ventricle	heart
33	chr20:41816800-41817200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
34	chr20:41816800-41817200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
35	chr20:41816800-41817200	Bivalent Enhancer	Right Ventricle	heart
36	chr20:41816800-41817200	ZNF genes & repeats	Spleen	Spleen
37	chr20:41816800-41817400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
38	chr20:41816800-41817400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
39	chr20:41816800-41818000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr20:41816800-41818000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
41	chr20:41816800-41818200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
42	chr20:41816800-41818200	Bivalent Enhancer	Colon Smooth Muscle	Colon
43	chr20:41816800-41818200	Bivalent/Poised TSS	Fetal Thymus	thymus
44	chr20:41817000-41817200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
45	chr20:41817000-41817200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr20:41817000-41817200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr20:41817000-41817200	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr20:41817000-41817200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
49	chr20:41817000-41817200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
50	chr20:41817000-41817200	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney

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