Variant report

Variant	rs59258634
Chromosome Location	chr20:13201111-13201112
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	MAX	chr20:13200483-13201847	H1-hESC	embryonic stem cell:	n/a	chr20:13201811-13201821
2	EGR1	chr20:13200623-13201132	H1-hESC	embryonic stem cell:	n/a	chr20:13201019-13201026
3	MAX	chr20:13200483-13201854	H1-hESC	embryonic stem cell:	n/a	chr20:13201811-13201821
4	ZNF143	chr20:13200690-13201484	H1-hESC	embryonic stem cell:	n/a	chr20:13200789-13200799 chr20:13201398-13201416 chr20:13201452-13201462 chr20:13200825-13200843
5	BACH1	chr20:13200843-13201401	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr20:13200479-13201519	A549	lung:	n/a	n/a
7	MXI1	chr20:13200661-13201113	H1-hESC	embryonic stem cell:	n/a	n/a
8	CREB1	chr20:13200585-13201271	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr20:13200407-13201585	A549	lung:	n/a	n/a
10	MAX	chr20:13200605-13201378	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr20:13200292-13201319	H1-neurons	neurons:	n/a	n/a
12	ZNF263	chr20:13200617-13202873	HEK293-T-REx	kidney:	n/a	chr20:13202352-13202361 chr20:13201867-13201888 chr20:13200798-13200807
13	E2F6	chr20:13200473-13201929	H1-hESC	embryonic stem cell:	n/a	chr20:13200473-13200480 chr20:13200707-13200714 chr20:13200707-13200714 chr20:13200703-13200715 chr20:13201661-13201668 chr20:13200707-13200714 chr20:13201736-13201745
14	E2F6	chr20:13200224-13201896	H1-hESC	embryonic stem cell:	n/a	chr20:13200473-13200480 chr20:13200707-13200714 chr20:13200707-13200714 chr20:13200703-13200715 chr20:13201661-13201668 chr20:13200707-13200714 chr20:13201736-13201745
15	E2F6	chr20:13200417-13201735	A549	lung:	n/a	chr20:13200473-13200480 chr20:13200707-13200714 chr20:13200707-13200714 chr20:13200703-13200715 chr20:13201661-13201668 chr20:13200707-13200714
16	MAX	chr20:13200564-13201254	H1-hESC	embryonic stem cell:	n/a	n/a
17	E2F6	chr20:13200533-13201334	A549	lung:	n/a	chr20:13200707-13200714 chr20:13200707-13200714 chr20:13200703-13200715 chr20:13200707-13200714
18	CREB1	chr20:13200669-13201239	H1-hESC	embryonic stem cell:	n/a	n/a
19	GABPA	chr20:13200703-13201369	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTBP2	chr20:13200367-13201967	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr20:13200280-13201344	H1-neurons	neurons:	n/a	n/a
22	MAX	chr20:13200645-13203023	HepG2	liver:	n/a	chr20:13202046-13202056 chr20:13201811-13201821 chr20:13202734-13202745 chr20:13202734-13202745 chr20:13202170-13202180
23	TCF12	chr20:13200598-13201315	A549	lung:	n/a	n/a
24	MAX	chr20:13200807-13201200	A549	lung:	n/a	n/a
25	MAX	chr20:13200563-13201417	ECC-1	luminal epithelium:	n/a	n/a
26	MAX	chr20:13200556-13202991	HepG2	liver:	n/a	chr20:13202046-13202056 chr20:13201811-13201821 chr20:13202734-13202745 chr20:13202734-13202745 chr20:13202170-13202180
27	MAX	chr20:13200888-13201369	HepG2	liver:	n/a	n/a
28	SIN3A	chr20:13200506-13203458	H1-hESC	embryonic stem cell:	n/a	chr20:13202323-13202334 chr20:13201060-13201071 chr20:13200983-13200994 chr20:13202023-13202034 chr20:13202590-13202601 chr20:13202086-13202099 chr20:13201538-13201551
29	CHD2	chr20:13201013-13201213	HepG2	liver:	n/a	n/a
30	TEAD4	chr20:13200810-13201208	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ISM1	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17812227	0.90[AFR][1000 genomes]
rs57671773	0.88[AFR][1000 genomes]
rs6105049	0.95[EUR][1000 genomes]
rs6131446	0.85[ASN][1000 genomes]
rs6131449	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6131453	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6134806	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6134808	0.83[ASN][1000 genomes]
rs6134814	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6134815	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6134818	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6134819	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6134821	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057219	chr20:12729479-13338337	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv912684	chr20:12734299-13311983	Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1067036	chr20:12737436-13338337	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv3488304	chr20:12738054-13341279	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv3488305	chr20:12738054-13341279	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv518184	chr20:12743808-13344672	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1063587	chr20:12756524-13330103	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv544185	chr20:12756524-13330103	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv916296	chr20:12756605-13329940	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv1067720	chr20:12756725-13329963	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv532513	chr20:12756725-13329963	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1064901	chr20:12773504-13318421	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	esv3425983	chr20:13046768-13461834	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv912685	chr20:13134768-13234124	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13199800-13201400	Bivalent Enhancer	Fetal Brain Male	brain
2	chr20:13199800-13201600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr20:13199800-13201800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr20:13199800-13203400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
5	chr20:13199800-13203600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr20:13200000-13201200	Bivalent Enhancer	Fetal Heart	heart
7	chr20:13200000-13201400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr20:13200000-13201600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr20:13200000-13203000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr20:13200000-13203600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
11	chr20:13200000-13203600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr20:13200000-13203600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
13	chr20:13200200-13201200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
14	chr20:13200200-13201200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
15	chr20:13200200-13201200	Bivalent Enhancer	Fetal Thymus	thymus
16	chr20:13200200-13201800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr20:13200200-13203000	Active TSS	Aorta	Aorta
18	chr20:13200200-13203200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr20:13200200-13203200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
20	chr20:13200400-13201200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
21	chr20:13200400-13201200	Flanking Bivalent TSS/Enh	NHEK	skin
22	chr20:13200400-13201400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr20:13200400-13201400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
24	chr20:13200400-13201400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr20:13200400-13201400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
26	chr20:13200400-13201400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
27	chr20:13200400-13201400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
28	chr20:13200400-13201400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
29	chr20:13200400-13201600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr20:13200400-13201600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
31	chr20:13200400-13201600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
32	chr20:13200400-13201800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr20:13200400-13201800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr20:13200400-13201800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr20:13200400-13201800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
36	chr20:13200400-13201800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
37	chr20:13200400-13201800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
38	chr20:13200600-13201200	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
39	chr20:13200600-13201200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
40	chr20:13200600-13201200	Bivalent Enhancer	Spleen	Spleen
41	chr20:13200600-13201400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr20:13200600-13201400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr20:13200600-13201400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
44	chr20:13200600-13201400	Flanking Active TSS	Pancreas	Pancrea
45	chr20:13200600-13201400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
46	chr20:13200600-13201400	Bivalent/Poised TSS	HSMM	muscle
47	chr20:13200600-13201600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
48	chr20:13200600-13201600	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
49	chr20:13200600-13201600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr20:13200600-13201600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin

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