Variant report

Variant	rs2293559
Chromosome Location	chr3:112738302-112738303
allele	A/C
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	POLR2A	chr3:112737462-112738876	GM18505	blood:	n/a	n/a
2	POLR2A	chr3:112737749-112739026	U87	brain:	n/a	n/a
3	YY1	chr3:112738230-112738618	HepG2	liver:	n/a	n/a
4	ZBTB7A	chr3:112737886-112738714	ECC-1	luminal epithelium:	n/a	chr3:112738267-112738274
5	TAF1	chr3:112737993-112738753	GM12878	blood:	n/a	n/a
6	MYC	chr3:112738150-112738847	H1-hESC	embryonic stem cell:	n/a	chr3:112738310-112738320
7	RCOR1	chr3:112738274-112739024	K562	blood:	n/a	n/a
8	TEAD4	chr3:112738273-112738749	K562	blood:	n/a	n/a
9	GABPA	chr3:112737831-112738916	MCF-7	breast:	n/a	chr3:112738311-112738320 chr3:112738262-112738271
10	MYC	chr3:112738075-112738387	HUVEC	blood vessel:	n/a	chr3:112738310-112738320
11	CREB1	chr3:112738095-112738817	A549	lung:	n/a	n/a
12	ELF1	chr3:112738191-112738685	A549	lung:	n/a	n/a
13	POLR2A	chr3:112737668-112738999	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr3:112737347-112738913	GM12878	blood:	n/a	n/a
15	MXI1	chr3:112738078-112738851	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr3:112737888-112739033	MCF-7	breast:	n/a	chr3:112738310-112738320
17	POLR2A	chr3:112737210-112739083	SK-N-MC	brain:	n/a	n/a
18	MAX	chr3:112737842-112739103	HepG2	liver:	n/a	chr3:112738310-112738320
19	YY1	chr3:112737994-112738641	GM12891	blood:	n/a	n/a
20	POLR2A	chr3:112737976-112738759	HepG2	liver:	n/a	n/a
21	POLR2A	chr3:112736649-112739006	GM12878	blood:	n/a	n/a
22	NR2C2	chr3:112737988-112738599	HepG2	liver:	n/a	n/a
23	POLR2A	chr3:112737122-112738647	GM12878	blood:	n/a	n/a
24	TAF1	chr3:112737943-112738668	H1-hESC	embryonic stem cell:	n/a	n/a
25	RUNX3	chr3:112738005-112739166	GM12878	blood:	n/a	n/a
26	NFIC	chr3:112737802-112738599	GM12878	blood:	n/a	n/a
27	SIN3AK20	chr3:112737950-112738313	HepG2	liver:	n/a	n/a
28	ELF1	chr3:112738202-112738739	A549	lung:	n/a	n/a
29	POLR2A	chr3:112737931-112738816	A549	lung:	n/a	n/a
30	POLR2A	chr3:112737507-112738795	GM12878	blood:	n/a	n/a
31	MXI1	chr3:112736597-112739325	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr3:112737944-112738823	MCF-7	breast:	n/a	n/a
33	MYC	chr3:112738007-112738802	MCF-7	breast:	n/a	chr3:112738310-112738320
34	POLR2A	chr3:112737951-112738842	HepG2	liver:	n/a	n/a
35	POLR2A	chr3:112737979-112738885	GM15510	blood:	n/a	n/a
36	POLR2A	chr3:112737644-112738856	Hela-S3	cervix:	n/a	n/a
37	GABPA	chr3:112738181-112738664	GM12878	blood:	n/a	chr3:112738311-112738320 chr3:112738262-112738271
38	YY1	chr3:112737912-112738824	GM12891	blood:	n/a	n/a
39	POLR2A	chr3:112738039-112738574	HepG2	liver:	n/a	n/a
40	GABPA	chr3:112737885-112738732	Hela-S3	cervix:	n/a	chr3:112738311-112738320 chr3:112738262-112738271
41	YY1	chr3:112737889-112738836	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:112737440-112738867	Hela-S3	cervix:	n/a	n/a
43	YY1	chr3:112737940-112738866	GM12878	blood:	n/a	n/a
44	STAT3	chr3:112737989-112738679	MCF10A-Er-Src	breast:	n/a	chr3:112738362-112738374
45	POLR2A	chr3:112737366-112738731	GM12891	blood:	n/a	n/a
46	MYC	chr3:112737773-112739493	A549	lung:	n/a	chr3:112738310-112738320
47	GABPA	chr3:112737790-112738962	MCF-7	breast:	n/a	chr3:112738311-112738320 chr3:112738262-112738271
48	E2F6	chr3:112738118-112738980	H1-hESC	embryonic stem cell:	n/a	chr3:112738607-112738617
49	MYC	chr3:112737716-112739051	K562	blood:	n/a	chr3:112738310-112738320
50	MYC	chr3:112738276-112738883	K562	blood:	n/a	chr3:112738310-112738320

No.	Distal block	Cell Line	Cell type
1	chr3:112709241..112710011-chr3:112737824..112738662,2	HCT-116	colon:
2	chr3:112726403..112732813-chr3:112735056..112739637,9	MCF-7	breast:
3	chr3:112709706..112712038-chr3:112736780..112739124,2	MCF-7	breast:
4	chr3:112738070..112738697-chr5:75013074..75013717,2	HCT-116	colon:
5	chr3:112358855..112360949-chr3:112737036..112738900,2	K562	blood:
6	chr3:112358697..112360499-chr3:112735766..112739410,3	MCF-7	breast:
7	chr3:112727442..112729984-chr3:112737783..112739677,2	MCF-7	breast:
8	chr3:112730174..112733803-chr3:112737181..112739606,5	MCF-7	breast:
9	chr3:112708671..112711453-chr3:112735992..112738475,2	K562	blood:
10	chr3:112358680..112360592-chr3:112737016..112739347,2	MCF-7	breast:
11	chr3:112737944..112740909-chr3:112760087..112762982,2	MCF-7	breast:
12	chr3:112279739..112282135-chr3:112735331..112738696,3	K562	blood:
13	chr3:112708547..112711309-chr3:112736671..112738787,3	MCF-7	breast:
14	chr3:112708559..112710573-chr3:112736590..112739999,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GTPBP8-1	chr3:112737048-112738553	NONHSAT091210

Variant related genes	Relation type
C3orf17	TF binding region
ENSG00000240057	TF binding region
ENSG00000144848	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000272844	Chromatin interaction
ENSG00000163608	Chromatin interaction
ENSG00000091986	Chromatin interaction
ENSG00000138459	Chromatin interaction
ENSG00000152359	Chromatin interaction
ENSG00000243483	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10934208	1.00[AFR][1000 genomes]
rs10934209	1.00[AFR][1000 genomes]
rs4146774	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56666099	1.00[AFR][1000 genomes]
rs56820451	1.00[AFR][1000 genomes]
rs57287136	1.00[AFR][1000 genomes]
rs57360909	1.00[AFR][1000 genomes]
rs58105957	1.00[AFR][1000 genomes]
rs60481719	1.00[AFR][1000 genomes]
rs60671920	1.00[AFR][1000 genomes]
rs61191442	1.00[AFR][1000 genomes]
rs61526975	1.00[AFR][1000 genomes]
rs61674636	1.00[AFR][1000 genomes]
rs6781014	0.86[ASN][1000 genomes]
rs72491118	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv1843165	chr3:112628205-112740145	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112736200-112738800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:112736600-112739000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:112736800-112738800	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr3:112737000-112738800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:112737000-112738800	Active TSS	GM12878-XiMat	blood
6	chr3:112737000-112738800	Active TSS	HSMMtube	muscle
7	chr3:112737000-112739000	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr3:112737000-112739000	Active TSS	Psoas Muscle	Psoas
9	chr3:112737000-112739000	Active TSS	Right Ventricle	heart
10	chr3:112737000-112739200	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr3:112737000-112739200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:112737000-112739200	Active TSS	Fetal Muscle Trunk	muscle
13	chr3:112737200-112738600	Active TSS	Fetal Intestine Small	intestine
14	chr3:112737200-112738800	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr3:112737200-112738800	Active TSS	H1 Cell Line	embryonic stem cell
16	chr3:112737200-112738800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:112737200-112738800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:112737200-112738800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:112737200-112738800	Active TSS	NHDF-Ad	bronchial
20	chr3:112737200-112739000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:112737200-112739000	Active TSS	Aorta	Aorta
22	chr3:112737200-112739000	Active TSS	Colonic Mucosa	Colon
23	chr3:112737200-112739200	Active TSS	Right Atrium	heart
24	chr3:112737200-112739200	Active TSS	A549	lung
25	chr3:112737200-112739200	Active TSS	HSMM	muscle
26	chr3:112737400-112738400	Bivalent/Poised TSS	HepG2	liver
27	chr3:112737400-112738600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:112737400-112738600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:112737400-112738600	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr3:112737400-112738600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:112737400-112738600	Active TSS	NHEK	skin
32	chr3:112737400-112738800	Active TSS	H9 Cell Line	embryonic stem cell
33	chr3:112737400-112738800	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr3:112737400-112738800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr3:112737400-112738800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:112737400-112738800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:112737400-112738800	Active TSS	Muscle Satellite Cultured Cells	--
38	chr3:112737400-112738800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:112737400-112738800	Active TSS	Fetal Intestine Large	intestine
40	chr3:112737400-112738800	Active TSS	Fetal Kidney	kidney
41	chr3:112737400-112738800	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr3:112737400-112738800	Active TSS	Fetal Stomach	stomach
43	chr3:112737400-112738800	Active TSS	Pancreas	Pancrea
44	chr3:112737400-112738800	Active TSS	NHLF	lung
45	chr3:112737400-112739000	Active TSS	Fetal Brain Female	brain
46	chr3:112737400-112739000	Active TSS	Left Ventricle	heart
47	chr3:112737400-112739000	Active TSS	Lung	lung
48	chr3:112737400-112739000	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr3:112737400-112739200	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr3:112737400-112739200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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