Variant report

Variant	rs201029374
Chromosome Location	chr2:56410941-56410942
allele	-/A
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	CHD2	chr2:56410725-56411442	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr2:56408936-56411912	K562	blood:	n/a	n/a
3	CTCF	chr2:56410735-56411006	Lung_OC	lung:	n/a	n/a
4	CTCF	chr2:56410646-56411048	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr2:56410726-56410989	T-47D	breast:	n/a	n/a
6	CTCF	chr2:56410650-56410989	A549	lung:	n/a	n/a
7	POLR2A	chr2:56410810-56412163	H1-neurons	neurons:	n/a	n/a
8	BHLHE40	chr2:56410720-56411023	GM12878	blood:	n/a	chr2:56410938-56410954
9	TEAD4	chr2:56410686-56412210	SK-N-SH	brain:	n/a	n/a
10	RCOR1	chr2:56410811-56411037	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr2:56410650-56410974	A549	lung:	n/a	n/a
12	HMGN3	chr2:56410736-56411790	K562	blood:	n/a	n/a
13	MYC	chr2:56410745-56411024	K562	blood:	n/a	n/a
14	POLR2A	chr2:56410670-56411469	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr2:56410736-56411061	ECC-1	luminal epithelium:	n/a	n/a
16	ZNF143	chr2:56410694-56411091	GM12878	blood:	n/a	n/a
17	CTCF	chr2:56410405-56411276	A549	lung:	n/a	n/a
18	CTCF	chr2:56410743-56410970	SK-N-SH_RA	brain:	n/a	n/a
19	ZMIZ1	chr2:56410794-56411011	K562	blood:	n/a	n/a
20	CTCF	chr2:56410706-56411006	Pancreas_OC	pancreas:	n/a	n/a
21	RAD21	chr2:56410725-56411042	K562	blood:	n/a	chr2:56410839-56410849 chr2:56410839-56410851 chr2:56410867-56410881
22	RUNX3	chr2:56410647-56411040	GM12878	blood:	n/a	n/a
23	CTCF	chr2:56410728-56410993	MCF-7	breast:	n/a	n/a
24	SIN3AK20	chr2:56410584-56411500	MCF-7	breast:	n/a	n/a
25	RAD21	chr2:56410567-56411274	HCT-116	colon:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
26	CTCF	chr2:56410691-56411208	K562	blood:	n/a	n/a
27	CTCF	chr2:56410730-56410989	GM10248	blood:	n/a	n/a
28	YY1	chr2:56410773-56411019	GM12878	blood:	n/a	n/a
29	ZNF143	chr2:56410701-56411037	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr2:56410619-56411036	HepG2	liver:	n/a	n/a
31	MAZ	chr2:56410701-56411300	K562	blood:	n/a	chr2:56411109-56411119
32	POLR2A	chr2:56410833-56411513	MCF-7	breast:	n/a	n/a
33	CTCF	chr2:56410569-56411145	MCF-7	breast:	n/a	n/a
34	CTCF	chr2:56410692-56411044	Fibrobl	skin:	n/a	n/a
35	RCOR1	chr2:56410686-56411205	K562	blood:	n/a	n/a
36	YY1	chr2:56410778-56411018	GM12891	blood:	n/a	n/a
37	YY1	chr2:56410685-56410984	GM12892	blood:	n/a	n/a
38	RAD21	chr2:56410617-56411211	MCF-7	breast:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
39	TBP	chr2:56410744-56411287	H1-hESC	embryonic stem cell:	n/a	n/a
40	RAD21	chr2:56410608-56411082	H1-hESC	embryonic stem cell:	n/a	chr2:56410839-56410849 chr2:56410839-56410851 chr2:56410867-56410881
41	CTCF	chr2:56410743-56410985	GM13976	blood:	n/a	n/a
42	ZKSCAN1	chr2:56410740-56411011	Hela-S3	cervix:	n/a	n/a
43	RAD21	chr2:56410711-56411052	GM12878	blood:	n/a	chr2:56410839-56410849 chr2:56410839-56410851 chr2:56410867-56410881
44	CTCF	chr2:56410718-56411007	Spleen_OC	spleen:	n/a	n/a
45	POLR2A	chr2:56410760-56411812	H1-neurons	neurons:	n/a	n/a
46	TAF1	chr2:56410673-56412158	SK-N-SH	brain:	n/a	n/a
47	REST	chr2:56410616-56411804	H1-neurons	neurons:	n/a	chr2:56411082-56411092 chr2:56411303-56411313 chr2:56410985-56411003 chr2:56411429-56411439 chr2:56411313-56411326 chr2:56411670-56411683 chr2:56411737-56411750
48	SMC3	chr2:56410656-56411141	Hela-S3	cervix:	n/a	chr2:56410966-56410976 chr2:56410867-56410881
49	MAX	chr2:56410730-56411047	Hela-S3	cervix:	n/a	n/a
50	RAD21	chr2:56410700-56410998	GM12878	blood:	n/a	chr2:56410839-56410849 chr2:56410839-56410851 chr2:56410867-56410881

Variant related genes	Relation type
CCDC85A	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv874162	chr2:56255832-56480571	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv874169	chr2:56383762-56473480	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2762648	chr2:56386656-56422448	Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3411625	chr2:56409873-56412421	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3442902	chr2:56410148-56412896	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3330480	chr2:56410673-56413221	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56409200-56411000	Enhancers	Placenta	Placenta
2	chr2:56409400-56411200	Weak transcription	Fetal Heart	heart
3	chr2:56409800-56411000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:56410000-56411000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
5	chr2:56410200-56411000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
6	chr2:56410400-56412800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:56410600-56411000	Bivalent Enhancer	Fetal Thymus	thymus
8	chr2:56410600-56411200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
9	chr2:56410600-56411200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:56410600-56411200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:56410600-56411200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:56410600-56411200	Active TSS	Right Ventricle	heart
13	chr2:56410600-56411400	Bivalent Enhancer	Stomach Mucosa	stomach
14	chr2:56410600-56411600	Active TSS	Lung	lung
15	chr2:56410600-56411600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
16	chr2:56410600-56411800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr2:56410600-56411800	Enhancers	Fetal Brain Male	brain
18	chr2:56410600-56411800	Active TSS	Fetal Brain Female	brain
19	chr2:56410600-56411800	Bivalent/Poised TSS	Fetal Stomach	stomach
20	chr2:56410600-56412000	Bivalent/Poised TSS	HepG2	liver
21	chr2:56410600-56412000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
22	chr2:56410600-56412600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
23	chr2:56410600-56412600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:56410600-56412800	Active TSS	HSMM	muscle
25	chr2:56410600-56413000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
26	chr2:56410600-56413000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:56410600-56413000	Active TSS	Muscle Satellite Cultured Cells	--
28	chr2:56410600-56413000	Active TSS	HSMMtube	muscle
29	chr2:56410600-56413200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr2:56410600-56413200	Active TSS	Brain Angular Gyrus	brain
31	chr2:56410600-56413400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
32	chr2:56410600-56413400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:56410600-56413400	Active TSS	Brain Hippocampus Middle	brain
34	chr2:56410600-56413400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:56410600-56413600	Active TSS	Psoas Muscle	Psoas
36	chr2:56410600-56413600	Active TSS	Right Atrium	heart
37	chr2:56410800-56411000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:56410800-56411000	Bivalent/Poised TSS	Primary B cells from cord blood	blood
39	chr2:56410800-56411000	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
40	chr2:56410800-56411000	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:56410800-56411000	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
42	chr2:56410800-56411000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:56410800-56411000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:56410800-56411000	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:56410800-56411000	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr2:56410800-56411000	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr2:56410800-56411000	Active TSS	Stomach Smooth Muscle	stomach
48	chr2:56410800-56411000	Bivalent/Poised TSS	Thymus	Thymus
49	chr2:56410800-56411000	Active TSS	HMEC	breast
50	chr2:56410800-56411000	Active TSS	NH-A	brain

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