Variant report

Variant	rs142674240
Chromosome Location	chr2:56411166-56411167
allele	A/G
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	chr2:56411080-56411230	BJ	skin:	n/a	n/a
4	POLR2A	chr2:56410810-56412163	H1-neurons	neurons:	n/a	n/a
5	TEAD4	chr2:56410686-56412210	SK-N-SH	brain:	n/a	n/a
6	HMGN3	chr2:56410736-56411790	K562	blood:	n/a	n/a
7	POLR2A	chr2:56410670-56411469	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr2:56410405-56411276	A549	lung:	n/a	n/a
9	SIN3AK20	chr2:56410584-56411500	MCF-7	breast:	n/a	n/a
10	RAD21	chr2:56410567-56411274	HCT-116	colon:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
11	CTCF	chr2:56410691-56411208	K562	blood:	n/a	n/a
12	MAZ	chr2:56410701-56411300	K562	blood:	n/a	chr2:56411109-56411119
13	POLR2A	chr2:56410833-56411513	MCF-7	breast:	n/a	n/a
14	RCOR1	chr2:56410686-56411205	K562	blood:	n/a	n/a
15	CTCF	chr2:56411040-56411190	AG04450	lung:	n/a	n/a
16	RAD21	chr2:56410617-56411211	MCF-7	breast:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
17	TBP	chr2:56410744-56411287	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr2:56411020-56411170	GM12872	blood:	n/a	n/a
19	POLR2A	chr2:56410760-56411812	H1-neurons	neurons:	n/a	n/a
20	TAF1	chr2:56410673-56412158	SK-N-SH	brain:	n/a	n/a
21	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
22	POLR2A	chr2:56410878-56411476	ProgFib	skin:	n/a	n/a
23	RAD21	chr2:56410582-56411217	H1-hESC	embryonic stem cell:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
24	RAD21	chr2:56410592-56411186	HepG2	liver:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
25	MAX	chr2:56410722-56411438	H1-hESC	embryonic stem cell:	n/a	chr2:56411109-56411119
26	RAD21	chr2:56410615-56411439	SK-N-SH	brain:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
27	UBTF	chr2:56410767-56411328	K562	blood:	n/a	n/a
28	MAX	chr2:56410628-56411241	SK-N-SH	brain:	n/a	chr2:56411109-56411119
29	RAD21	chr2:56410665-56411360	H1-hESC	embryonic stem cell:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
30	POLR2A	chr2:56410644-56412125	SK-N-SH	brain:	n/a	n/a
31	CTCF	chr2:56410666-56411249	MCF-7	breast:	n/a	n/a
32	PBX3	chr2:56410623-56411329	SK-N-SH	brain:	n/a	n/a
33	SIN3A	chr2:56410680-56412106	H1-hESC	embryonic stem cell:	n/a	chr2:56410802-56410810 chr2:56411313-56411326 chr2:56410910-56410918 chr2:56412066-56412077 chr2:56411082-56411091 chr2:56411456-56411469
34	SIN3AK20	chr2:56410618-56411440	SK-N-SH	brain:	n/a	n/a
35	SMC3	chr2:56410683-56411207	K562	blood:	n/a	chr2:56410966-56410976 chr2:56410867-56410881
36	HA-E2F1	chr2:56410713-56413226	MCF-7	breast:	n/a	chr2:56411453-56411460 chr2:56412055-56412064 chr2:56412483-56412494 chr2:56412097-56412107 chr2:56411453-56411460 chr2:56410964-56410973 chr2:56411304-56411314 chr2:56411610-56411619 chr2:56412093-56412102 chr2:56411453-56411460 chr2:56411692-56411701 chr2:56411223-56411233
37	POLR2A	chr2:56410717-56412018	HUVEC	blood vessel:	n/a	n/a
38	MAX	chr2:56410691-56411377	ECC-1	luminal epithelium:	n/a	chr2:56411109-56411119
39	MAX	chr2:56410659-56411323	MCF-7	breast:	n/a	chr2:56411109-56411119
40	POLR2A	chr2:56410625-56411483	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr2:56410941-56411440	Gliobla	brain:	n/a	n/a
42	POLR2A	chr2:56410906-56412143	SK-N-SH	brain:	n/a	n/a
43	MAX	chr2:56410652-56411275	SK-N-SH	brain:	n/a	chr2:56411109-56411119
44	RAD21	chr2:56410664-56411288	SK-N-SH_RA	brain:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
45	POLR2A	chr2:56410759-56413309	HUVEC	blood vessel:	n/a	n/a
46	ZNF263	chr2:56410709-56413339	HEK293-T-REx	kidney:	n/a	chr2:56412088-56412097
47	RAD21	chr2:56410645-56411248	ECC-1	luminal epithelium:	n/a	chr2:56410839-56410849 chr2:56411078-56411092 chr2:56410839-56410851 chr2:56410867-56410881
48	MAZ	chr2:56410617-56411517	IMR90	lung:	n/a	chr2:56411109-56411119
49	CTCF	chr2:56410591-56411226	HCT-116	colon:	n/a	n/a
50	POLR2A	chr2:56410880-56411325	HUVEC	blood vessel:	n/a	n/a

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:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56409400-56411200	Weak transcription	Fetal Heart	heart
2	chr2:56410400-56412800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:56410600-56411200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
4	chr2:56410600-56411200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:56410600-56411200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:56410600-56411200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:56410600-56411200	Active TSS	Right Ventricle	heart
8	chr2:56410600-56411400	Bivalent Enhancer	Stomach Mucosa	stomach
9	chr2:56410600-56411600	Active TSS	Lung	lung
10	chr2:56410600-56411600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
11	chr2:56410600-56411800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr2:56410600-56411800	Enhancers	Fetal Brain Male	brain
13	chr2:56410600-56411800	Active TSS	Fetal Brain Female	brain
14	chr2:56410600-56411800	Bivalent/Poised TSS	Fetal Stomach	stomach
15	chr2:56410600-56412000	Bivalent/Poised TSS	HepG2	liver
16	chr2:56410600-56412000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
17	chr2:56410600-56412600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr2:56410600-56412600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:56410600-56412800	Active TSS	HSMM	muscle
20	chr2:56410600-56413000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
21	chr2:56410600-56413000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:56410600-56413000	Active TSS	Muscle Satellite Cultured Cells	--
23	chr2:56410600-56413000	Active TSS	HSMMtube	muscle
24	chr2:56410600-56413200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
25	chr2:56410600-56413200	Active TSS	Brain Angular Gyrus	brain
26	chr2:56410600-56413400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr2:56410600-56413400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:56410600-56413400	Active TSS	Brain Hippocampus Middle	brain
29	chr2:56410600-56413400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:56410600-56413600	Active TSS	Psoas Muscle	Psoas
31	chr2:56410600-56413600	Active TSS	Right Atrium	heart
32	chr2:56410800-56411200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:56410800-56411200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:56410800-56411200	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr2:56410800-56411200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
36	chr2:56410800-56411200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
37	chr2:56410800-56411200	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:56410800-56411200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:56410800-56411200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:56410800-56411200	Active TSS	Adipose Nuclei	Adipose
41	chr2:56410800-56411200	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr2:56410800-56411200	Active TSS	Ovary	ovary
43	chr2:56410800-56411200	Active TSS	Pancreas	Pancrea
44	chr2:56410800-56411200	Bivalent/Poised TSS	NHLF	lung
45	chr2:56410800-56411400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr2:56410800-56411400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:56410800-56411400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
48	chr2:56410800-56411400	Active TSS	Brain Germinal Matrix	brain
49	chr2:56410800-56411400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
50	chr2:56410800-56411400	Active TSS	Esophagus	oesophagus

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