Variant report

Variant	rs554038925
Chromosome Location	chr5:74162229-74162230
allele	C/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	POLR2A	chr5:74161586-74162464	A549	lung:	n/a	n/a
2	ZBTB7A	chr5:74161392-74162921	ECC-1	luminal epithelium:	n/a	chr5:74162413-74162422 chr5:74162253-74162264
3	MAZ	chr5:74162144-74162296	GM12878	blood:	n/a	chr5:74162270-74162280
4	POLR2A	chr5:74160377-74163048	HepG2	liver:	n/a	n/a
5	YY1	chr5:74162065-74162320	GM12891	blood:	n/a	chr5:74162250-74162264
6	MAX	chr5:74161188-74163068	HepG2	liver:	n/a	chr5:74162270-74162280 chr5:74162396-74162406
7	POLR2A	chr5:74161468-74162445	ECC-1	luminal epithelium:	n/a	n/a
8	CTCF	chr5:74162167-74162249	Gliobla	brain:	n/a	n/a
9	POLR2A	chr5:74161026-74163038	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr5:74161985-74162899	HepG2	liver:	n/a	n/a
11	TCF7L2	chr5:74162030-74162952	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr5:74160806-74162477	MCF10A-Er-Src	breast:	n/a	n/a
13	CTCF	chr5:74162100-74162250	SK-N-SH_RA	brain:	n/a	n/a
14	POLR2A	chr5:74161937-74162427	GM12878	blood:	n/a	n/a
15	MXI1	chr5:74161189-74163023	HepG2	liver:	n/a	n/a
16	SIN3AK20	chr5:74161541-74162445	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr5:74161305-74162851	HCT-116	colon:	n/a	n/a
18	CTCF	chr5:74162168-74162253	H1-hESC	embryonic stem cell:	n/a	n/a
19	RAD21	chr5:74161531-74162262	H1-hESC	embryonic stem cell:	n/a	chr5:74161852-74161865 chr5:74161751-74161761 chr5:74161749-74161762 chr5:74161750-74161759
20	POLR2A	chr5:74161505-74162913	HCT-116	colon:	n/a	n/a
21	POLR2A	chr5:74160759-74163043	HepG2	liver:	n/a	n/a
22	TCF7L2	chr5:74161511-74162958	HCT-116	colon:	n/a	n/a
23	ZBTB7A	chr5:74162111-74162445	HepG2	liver:	n/a	chr5:74162413-74162422 chr5:74162253-74162264
24	CTCF	chr5:74162109-74162275	NHEK	skin:	n/a	n/a
25	CEBPD	chr5:74161985-74162435	HepG2	liver:	n/a	n/a
26	YY1	chr5:74161277-74162398	H1-hESC	embryonic stem cell:	n/a	chr5:74161820-74161834 chr5:74161851-74161865 chr5:74161678-74161692 chr5:74161707-74161729 chr5:74161684-74161693 chr5:74162250-74162264
27	ZNF263	chr5:74160620-74162789	HEK293-T-REx	kidney:	n/a	n/a
28	MAX	chr5:74161443-74162607	ECC-1	luminal epithelium:	n/a	chr5:74162270-74162280 chr5:74162396-74162406
29	CTBP2	chr5:74161126-74162967	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr5:74161120-74162928	H1-hESC	embryonic stem cell:	n/a	n/a
31	ZBTB7A	chr5:74162160-74162448	HepG2	liver:	n/a	chr5:74162413-74162422 chr5:74162253-74162264
32	POLR2A	chr5:74161267-74162738	HEK293	kidney:	n/a	n/a
33	POLR2A	chr5:74161389-74162762	MCF-7	breast:	n/a	n/a
34	NFIC	chr5:74161468-74162326	ECC-1	luminal epithelium:	n/a	n/a
35	HEY1	chr5:74161427-74163052	HepG2	liver:	n/a	chr5:74161997-74162012 chr5:74162243-74162258 chr5:74162276-74162291 chr5:74162345-74162360
36	POLR2A	chr5:74161463-74162581	HCT-116	colon:	n/a	n/a
37	CTCF	chr5:74162033-74162300	MCF-7	breast:	n/a	n/a
38	POLR2A	chr5:74161992-74162353	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr5:74162100-74162250	SAEC	small airway:	n/a	n/a
40	CREB1	chr5:74161764-74162679	A549	lung:	n/a	n/a
41	MAX	chr5:74161427-74162348	MCF-7	breast:	n/a	chr5:74162270-74162280
42	POLR2A	chr5:74161888-74162381	GM12891	blood:	n/a	n/a
43	CTCF	chr5:74162150-74162236	GM19239	blood:	n/a	n/a
44	MYC	chr5:74162096-74162229	MCF-7	breast:	n/a	n/a
45	TBP	chr5:74161255-74163024	H1-hESC	embryonic stem cell:	n/a	n/a
46	TAF1	chr5:74162003-74162915	H1-neurons	neurons:	n/a	n/a
47	REST	chr5:74160888-74163163	H1-neurons	neurons:	n/a	chr5:74161964-74161977 chr5:74161838-74161851 chr5:74161891-74161909
48	TAF1	chr5:74161561-74162461	HepG2	liver:	n/a	n/a
49	TAF1	chr5:74162134-74162602	H1-neurons	neurons:	n/a	n/a
50	HDAC2	chr5:74161560-74163061	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:74162223-74162273	U87	brain:	n/a
2	chr5:74162223-74162273	AG10803	skin:	n/a
3	chr5:74162223-74162273	HMEC	breast:	n/a
4	chr5:74162223-74162273	HCT-116	colon:	n/a
5	chr5:74162223-74162273	AG04449	skin:	fetal
6	chr5:74162223-74162273	HUVEC	blood vessel:	n/a
7	chr5:74162223-74162273	GM12878	blood:	n/a
8	chr5:74162223-74162273	ECC-1	luminal epithelium:	n/a
9	chr5:74162223-74162273	HepG2	liver:	n/a
10	chr5:74162223-74162273	MCF10A-Er-Src	breast:	n/a
11	chr5:74162223-74162273	GM12891	blood:	n/a
12	chr5:74162223-74162273	Caco-2	colon:	n/a
13	chr5:74162223-74162273	HL-60	blood:	n/a
14	chr5:74162223-74162273	Hepatocyte	liver:	n/a
15	chr5:74162223-74162273	K562	blood:	n/a
16	chr5:74162223-74162273	BJ	skin:	n/a
17	chr5:74162223-74162273	AG04450	lung:	fetal
18	chr5:74162223-74162273	ovcar-3	ovarian:	n/a
19	chr5:74162223-74162273	GM12892	blood:	n/a
20	chr5:74162223-74162273	SK-N-SH_RA	brain:	n/a
21	chr5:74162223-74162273	SKMC	muscle:	n/a
22	chr5:74162223-74162273	MCF-7	breast:	n/a
23	chr5:74162223-74162273	HIPEpiC	eye:	n/a
24	chr5:74162223-74162273	NHBE	bronchial:	n/a
25	chr5:74162223-74162273	HCF	heart:	n/a
26	chr5:74162223-74162273	Hela-S3	cervix:	n/a
27	chr5:74162223-74162273	T-47D	breast:	n/a
28	chr5:74162223-74162273	GM06990	blood:	n/a
29	chr5:74162223-74162273	AG09319	gingival:	n/a
30	chr5:74162223-74162273	HEEpiC	esophagus:	n/a
31	chr5:74162223-74162273	HRE	kidney:	n/a
32	chr5:74162223-74162273	RPTEC	kidney:	n/a
33	chr5:74162223-74162273	HNPCEpiC	eye:	n/a
34	chr5:74162223-74162273	HPAEpiC	pulmonary alveolar:	n/a
35	chr5:74162223-74162273	ProgFib	skin:	n/a
36	chr5:74162223-74162273	HRPEpiC	eye:	n/a
37	chr5:74162223-74162273	NT2-D1	testis:	n/a
38	chr5:74162223-74162273	A549	lung:	n/a
39	chr5:74162223-74162273	NH-A	brain:	n/a
40	chr5:74162223-74162273	Jurkat	blood:	n/a
41	chr5:74162223-74162273	NHDF-neo	bronchial:	n/a
42	chr5:74162223-74162273	SAEC	small airway:	n/a
43	chr5:74162223-74162273	H1-hESC	embryonic stem cell:	embryo
44	chr5:74162223-74162273	AoSMC	blood vessel:	n/a
45	chr5:74162223-74162273	SK-N-SH	brain:	n/a
46	chr5:74162223-74162273	SK-N-MC	brain:	n/a
47	chr5:74162223-74162273	BE2_C	brain:	n/a
48	chr5:74162223-74162273	HCM	heart:	n/a
49	chr5:74162223-74162273	HEK293	kidney:	embryo
50	chr5:74162223-74162273	PANC-1	pancreas:	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NSA2-6	chr5:74161718-74163679	ENSG00000271714.1

Variant related genes	Relation type
FAM169A	TF binding region
FAM169A	CpG island

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3338870	chr5:74159996-74164294	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3502490	chr5:74160996-74163344	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv3502491	chr5:74160996-74163344	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74158600-74163000	Active TSS	H1 Cell Line	embryonic stem cell
2	chr5:74158800-74163800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:74159000-74162800	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr5:74159400-74163000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:74159400-74163000	Active TSS	H9 Cell Line	embryonic stem cell
6	chr5:74159400-74163800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr5:74159600-74162800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:74159800-74163000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:74160000-74162800	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr5:74160000-74163000	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr5:74160200-74163000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:74160200-74163000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr5:74160400-74162800	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr5:74160400-74163000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:74160400-74163000	Active TSS	Brain Angular Gyrus	brain
16	chr5:74160400-74163200	Active TSS	Brain Cingulate Gyrus	brain
17	chr5:74160600-74162600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:74160600-74163000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr5:74160600-74163000	Active TSS	Fetal Kidney	kidney
20	chr5:74160600-74163000	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr5:74160800-74162600	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr5:74160800-74162800	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr5:74160800-74162800	Active TSS	Brain Substantia Nigra	brain
24	chr5:74160800-74163000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:74160800-74163000	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr5:74160800-74163000	Active TSS	Brain Anterior Caudate	brain
27	chr5:74161000-74162400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:74161000-74162600	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr5:74161000-74162600	Active TSS	HMEC	breast
30	chr5:74161000-74163000	Active TSS	Ovary	ovary
31	chr5:74161000-74163000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
32	chr5:74161200-74162600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr5:74161200-74162600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr5:74161200-74162600	Active TSS	Gastric	stomach
35	chr5:74161200-74162600	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
36	chr5:74161200-74162800	Active TSS	HSMM	muscle
37	chr5:74161200-74162800	Active TSS	HSMMtube	muscle
38	chr5:74161200-74162800	Bivalent/Poised TSS	Osteobl	bone
39	chr5:74161400-74162400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr5:74161400-74162400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr5:74161400-74162400	Active TSS	NHEK	skin
42	chr5:74161400-74162600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr5:74161400-74162600	Active TSS	Aorta	Aorta
44	chr5:74161400-74162600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
45	chr5:74161400-74162600	Active TSS	Brain Hippocampus Middle	brain
46	chr5:74161400-74162600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
47	chr5:74161400-74162600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
48	chr5:74161400-74162600	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
49	chr5:74161400-74162600	Bivalent/Poised TSS	NHLF	lung
50	chr5:74161400-74162800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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