Variant report

Variant	rs2940928
Chromosome Location	chr5:42423905-42423906
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	TBP	chr5:42423384-42423940	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr5:42423329-42423993	ECC-1	luminal epithelium:	n/a	n/a
3	RFX5	chr5:42423097-42423940	SK-N-SH	brain:	n/a	chr5:42423587-42423602 chr5:42423351-42423364
4	HA-E2F1	chr5:42423408-42425524	MCF-7	breast:	n/a	n/a
5	MAX	chr5:42423360-42424141	H1-hESC	embryonic stem cell:	n/a	n/a
6	YY1	chr5:42423473-42424086	HepG2	liver:	n/a	n/a
7	YY1	chr5:42423360-42423987	H1-hESC	embryonic stem cell:	n/a	n/a
8	ZNF263	chr5:42423144-42425027	HEK293-T-REx	kidney:	n/a	chr5:42424219-42424228 chr5:42423858-42423867
9	E2F6	chr5:42423895-42424051	K562	blood:	n/a	n/a
10	RCOR1	chr5:42423249-42424011	IMR90	lung:	n/a	n/a
11	YY1	chr5:42423624-42424023	ECC-1	luminal epithelium:	n/a	n/a
12	FOXP2	chr5:42423477-42423920	PFSK-1	brain:	n/a	n/a
13	E2F6	chr5:42423597-42424958	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr5:42423012-42423907	A549	lung:	n/a	chr5:42423514-42423532
15	E2F6	chr5:42423316-42424213	H1-hESC	embryonic stem cell:	n/a	n/a
16	REST	chr5:42423126-42424302	H1-neurons	neurons:	n/a	chr5:42423566-42423576
17	MAX	chr5:42423375-42424082	H1-hESC	embryonic stem cell:	n/a	n/a
18	BACH1	chr5:42423411-42424197	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr5:42423392-42424072	H1-neurons	neurons:	n/a	n/a
20	SIN3A	chr5:42423332-42425259	H1-hESC	embryonic stem cell:	n/a	chr5:42424836-42424849
21	CTCF	chr5:42423188-42424195	SK-N-SH	brain:	n/a	chr5:42423514-42423532
22	RAD21	chr5:42423096-42423931	SK-N-SH	brain:	n/a	chr5:42423724-42423734
23	POLR2A	chr5:42423499-42423943	Gliobla	brain:	n/a	n/a
24	MAZ	chr5:42423484-42423917	HepG2	liver:	n/a	n/a
25	MYC	chr5:42423524-42423940	MCF-7	breast:	n/a	n/a
26	SMC3	chr5:42423174-42423924	SK-N-SH	brain:	n/a	chr5:42423724-42423738
27	MXI1	chr5:42423284-42423978	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
GHR	TF binding region

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10755268	0.82[EUR][1000 genomes]
rs13162973	0.82[EUR][1000 genomes]
rs1396773	0.82[EUR][1000 genomes]
rs1509455	0.81[EUR][1000 genomes]
rs1509456	0.81[EUR][1000 genomes]
rs1567374	0.82[EUR][1000 genomes]
rs1858137	0.82[EUR][1000 genomes]
rs1876788	0.82[EUR][1000 genomes]
rs1876790	0.81[EUR][1000 genomes]
rs1912107	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2175126	0.85[AMR][1000 genomes]
rs2940912	0.81[EUR][1000 genomes]
rs2940929	0.81[EUR][1000 genomes]
rs2972395	0.82[EUR][1000 genomes]
rs2972400	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2972415	0.81[EUR][1000 genomes]
rs4642376	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4866890	0.82[EUR][1000 genomes]
rs6451614	0.82[EUR][1000 genomes]
rs6881436	0.80[EUR][1000 genomes]
rs7379192	0.82[EUR][1000 genomes]
rs7704355	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9686286	0.81[EUR][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	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv881375	chr5:42254097-42442715	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv948514	chr5:42270161-42519262	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42423000-42424400	Active TSS	H9 Cell Line	embryonic stem cell
2	chr5:42423000-42424600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:42423000-42425000	Active TSS	Left Ventricle	heart
4	chr5:42423000-42425400	Active TSS	NHLF	lung
5	chr5:42423000-42426000	Active TSS	Right Atrium	heart
6	chr5:42423200-42424000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:42423200-42424200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:42423200-42424200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:42423200-42424200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:42423200-42424200	Enhancers	Fetal Brain Male	brain
11	chr5:42423200-42424400	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
12	chr5:42423200-42424400	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr5:42423200-42424400	Active TSS	Fetal Brain Female	brain
14	chr5:42423200-42424400	Active TSS	Fetal Muscle Trunk	muscle
15	chr5:42423200-42424600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:42423200-42424600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:42423200-42424600	Active TSS	Adipose Nuclei	Adipose
18	chr5:42423200-42424600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr5:42423200-42424600	Active TSS	Fetal Intestine Small	intestine
20	chr5:42423200-42424600	Active TSS	Pancreas	Pancrea
21	chr5:42423200-42424800	Active TSS	Brain Anterior Caudate	brain
22	chr5:42423200-42424800	Active TSS	Colonic Mucosa	Colon
23	chr5:42423200-42424800	Active TSS	Duodenum Mucosa	Duodenum
24	chr5:42423200-42424800	Active TSS	Placenta Amnion	Placenta Amnion
25	chr5:42423200-42425000	Active TSS	Brain Substantia Nigra	brain
26	chr5:42423200-42425000	Active TSS	Ovary	ovary
27	chr5:42423200-42425000	Active TSS	Right Ventricle	heart
28	chr5:42423200-42425000	Bivalent/Poised TSS	A549	lung
29	chr5:42423200-42425200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:42423200-42425200	Active TSS	Aorta	Aorta
31	chr5:42423200-42425200	Active TSS	Psoas Muscle	Psoas
32	chr5:42423200-42425400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr5:42423200-42425400	Active TSS	Colon Smooth Muscle	Colon
34	chr5:42423200-42425400	Active TSS	Esophagus	oesophagus
35	chr5:42423200-42425400	Active TSS	NHDF-Ad	bronchial
36	chr5:42423400-42424000	Active TSS	H1 Cell Line	embryonic stem cell
37	chr5:42423400-42424000	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr5:42423400-42424000	Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr5:42423400-42424000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:42423400-42424000	Bivalent/Poised TSS	HepG2	liver
41	chr5:42423400-42424000	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
42	chr5:42423400-42424200	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr5:42423400-42424200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:42423400-42424200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
45	chr5:42423400-42424200	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr5:42423400-42424200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr5:42423400-42424200	Active TSS	Stomach Mucosa	stomach
48	chr5:42423400-42424200	Active TSS	HMEC	breast
49	chr5:42423400-42424400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr5:42423400-42424400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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