Variant report

Variant	rs62140778
Chromosome Location	chr2:58654944-58654945
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	YY1	chr2:58654857-58655643	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr2:58654590-58655185	MCF-7	breast:	n/a	n/a
3	POU2F2	chr2:58654701-58654956	GM12891	blood:	n/a	chr2:58654770-58654791 chr2:58654777-58654787 chr2:58654775-58654786 chr2:58654774-58654789 chr2:58654778-58654785 chr2:58654777-58654787 chr2:58654776-58654788 chr2:58654777-58654786 chr2:58654776-58654786 chr2:58654777-58654785 chr2:58654772-58654790
4	MAX	chr2:58654613-58655407	A549	lung:	n/a	n/a
5	POLR2A	chr2:58654580-58656569	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr2:58654370-58656704	H1-hESC	embryonic stem cell:	n/a	n/a
7	HA-E2F1	chr2:58654626-58655583	MCF-7	breast:	n/a	chr2:58654865-58654874
8	REST	chr2:58654592-58654985	H1-hESC	embryonic stem cell:	n/a	n/a
9	REST	chr2:58654655-58655000	Hela-S3	cervix:	n/a	n/a
10	MAX	chr2:58654732-58655587	H1-hESC	embryonic stem cell:	n/a	n/a
11	REST	chr2:58654629-58654979	Hela-S3	cervix:	n/a	n/a
12	TAF7	chr2:58654742-58655238	H1-hESC	embryonic stem cell:	n/a	n/a
13	REST	chr2:58654559-58655073	H1-hESC	embryonic stem cell:	n/a	n/a
14	RAD21	chr2:58654623-58655182	H1-hESC	embryonic stem cell:	n/a	n/a
15	REST	chr2:58654583-58655044	PFSK-1	brain:	n/a	n/a
16	TBP	chr2:58654751-58656508	H1-hESC	embryonic stem cell:	n/a	n/a
17	YY1	chr2:58654669-58655629	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTBP2	chr2:58654675-58655588	H1-hESC	embryonic stem cell:	n/a	n/a
19	REST	chr2:58654474-58655213	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr2:58654936-58654990	MCF10A-Er-Src	breast:	n/a	n/a
21	MAX	chr2:58654616-58655401	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr2:58654840-58655124	MCF-7	breast:	n/a	n/a
23	BRCA1	chr2:58654842-58655007	HepG2	liver:	n/a	n/a
24	BACH1	chr2:58654529-58655113	H1-hESC	embryonic stem cell:	n/a	n/a
25	HDAC2	chr2:58654688-58655001	H1-hESC	embryonic stem cell:	n/a	chr2:58654813-58654832 chr2:58654864-58654873 chr2:58654866-58654875
26	MAFK	chr2:58654892-58655274	HepG2	liver:	n/a	chr2:58655043-58655058
27	TCF12	chr2:58654781-58655414	A549	lung:	n/a	n/a
28	MAX	chr2:58654640-58655337	ECC-1	luminal epithelium:	n/a	n/a
29	REST	chr2:58654447-58655271	A549	lung:	n/a	n/a
30	REST	chr2:58654557-58655027	GM12878	blood:	n/a	n/a
31	GTF2F1	chr2:58654724-58655049	H1-hESC	embryonic stem cell:	n/a	n/a
32	HNF4A	chr2:58654889-58655185	HepG2	liver:	n/a	n/a
33	MAFK	chr2:58654706-58655182	H1-hESC	embryonic stem cell:	n/a	chr2:58655043-58655058
34	POLR2A	chr2:58654825-58655246	H1-hESC	embryonic stem cell:	n/a	n/a
35	RAD21	chr2:58654810-58655530	H1-hESC	embryonic stem cell:	n/a	n/a
36	ZNF263	chr2:58654671-58655421	HEK293-T-REx	kidney:	n/a	n/a
37	TAF1	chr2:58654730-58655655	H1-hESC	embryonic stem cell:	n/a	n/a
38	TEAD4	chr2:58654563-58655084	A549	lung:	n/a	n/a
39	REST	chr2:58654656-58655049	PANC-1	pancreas:	n/a	n/a
40	E2F6	chr2:58654850-58655310	A549	lung:	n/a	chr2:58654865-58654874
41	REST	chr2:58654656-58655003	K562	blood:	n/a	n/a
42	MYC	chr2:58654895-58655026	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr2:58654783-58657002	H1-neurons	neurons:	n/a	n/a
44	MAX	chr2:58654544-58655421	A549	lung:	n/a	n/a
45	MAFF	chr2:58654903-58655222	HepG2	liver:	n/a	chr2:58655042-58655060
46	POLR2A	chr2:58654903-58655019	A549	lung:	n/a	n/a
47	POLR2A	chr2:58654927-58655004	ProgFib	skin:	n/a	n/a
48	HDAC2	chr2:58654724-58655173	MCF-7	breast:	n/a	chr2:58654813-58654832 chr2:58654864-58654873 chr2:58654866-58654875
49	POLR2A	chr2:58654746-58655651	H1-hESC	embryonic stem cell:	n/a	n/a
50	CHD1	chr2:58654580-58655502	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VRK2-5	chr2:58654934-58655115	ENSG00000233723

Variant related genes	Relation type
LINC01122	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10490245	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41423548	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57174143	0.89[ASN][1000 genomes]
rs57335427	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60975403	0.86[ASN][1000 genomes]
rs62140783	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62140784	0.82[EUR][1000 genomes]
rs62140821	0.85[ASN][1000 genomes]
rs72813949	0.84[ASN][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	esv2755713	chr2:58653580-58782707	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3395723	chr2:58654473-58657321	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
3	esv3323812	chr2:58654573-58657096	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	esv3437316	chr2:58654648-58656446	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58654000-58655400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:58654200-58655000	Flanking Active TSS	Fetal Heart	heart
3	chr2:58654200-58655200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:58654200-58655200	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr2:58654200-58655400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr2:58654200-58655400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:58654200-58656000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:58654400-58655000	Bivalent Enhancer	Stomach Mucosa	stomach
9	chr2:58654400-58655200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:58654400-58656200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:58654400-58656200	Active TSS	Fetal Stomach	stomach
12	chr2:58654400-58656400	Active TSS	H1 Cell Line	embryonic stem cell
13	chr2:58654400-58656400	Active TSS	Fetal Brain Female	brain
14	chr2:58654400-58656600	Active TSS	NH-A	brain
15	chr2:58654400-58657000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:58654600-58655000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:58654600-58655000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:58654600-58655000	Flanking Active TSS	Brain Cingulate Gyrus	brain
19	chr2:58654600-58655000	Flanking Active TSS	Fetal Brain Male	brain
20	chr2:58654600-58655000	Flanking Active TSS	Fetal Intestine Large	intestine
21	chr2:58654600-58655000	Flanking Active TSS	Fetal Muscle Leg	muscle
22	chr2:58654600-58655000	Flanking Active TSS	Right Ventricle	heart
23	chr2:58654600-58655000	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr2:58654600-58655000	Bivalent/Poised TSS	NHEK	skin
25	chr2:58654600-58655200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr2:58654600-58655200	Flanking Active TSS	Colon Smooth Muscle	Colon
27	chr2:58654600-58655200	Flanking Active TSS	Fetal Thymus	thymus
28	chr2:58654600-58655200	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
29	chr2:58654600-58655200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr2:58654600-58655200	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr2:58654600-58655200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
32	chr2:58654600-58655400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
33	chr2:58654600-58655400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
34	chr2:58654600-58655400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:58654600-58655400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr2:58654600-58655400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:58654600-58655400	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
38	chr2:58654600-58655600	Active TSS	Hela-S3	cervix
39	chr2:58654600-58656000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:58654600-58656200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:58654600-58656200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:58654600-58656200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:58654600-58656200	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr2:58654600-58656200	Active TSS	Duodenum Mucosa	Duodenum
45	chr2:58654600-58656400	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr2:58654600-58656400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:58654600-58656400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr2:58654600-58656400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:58654600-58656400	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr2:58654600-58656400	Active TSS	Ovary	ovary

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