Variant report

Variant	rs539281972
Chromosome Location	chr6:33754766-33754767
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:33754660-33756447	PFSK-1	brain:	n/a	n/a
2	CHD1	chr6:33753489-33757327	IMR90	lung:	n/a	n/a
3	POLR2A	chr6:33754637-33757242	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr6:33754307-33756475	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr6:33753458-33754807	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr6:33754123-33757999	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr6:33754585-33758231	HepG2	liver:	n/a	n/a
8	POLR2A	chr6:33754388-33756268	K562	blood:	n/a	n/a
9	POLR2A	chr6:33754751-33757465	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr6:33754757-33755297	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:33754751-33754801	GM19239	blood:	n/a
2	chr6:33754751-33754801	AG04450	lung:	fetal
3	chr6:33754751-33754801	AG09319	gingival:	n/a
4	chr6:33754751-33754801	HAEpiC	amniotic membrane:	n/a
5	chr6:33754751-33754801	NB4	blood:	n/a
6	chr6:33754751-33754801	HCM	heart:	n/a
7	chr6:33754751-33754801	NHBE	bronchial:	n/a
8	chr6:33754751-33754801	HNPCEpiC	eye:	n/a
9	chr6:33754751-33754801	T-47D	breast:	n/a
10	chr6:33754751-33754801	NH-A	brain:	n/a
11	chr6:33754751-33754801	HEEpiC	esophagus:	n/a
12	chr6:33754751-33754801	GM06990	blood:	n/a
13	chr6:33754751-33754801	HCPEpiC	choroid plexus:	n/a
14	chr6:33754751-33754801	A549	lung:	n/a
15	chr6:33754751-33754801	CMK	blood:	n/a
16	chr6:33754751-33754801	AG04449	skin:	fetal
17	chr6:33754751-33754801	BJ	skin:	n/a
18	chr6:33754751-33754801	HepG2	liver:	n/a
19	chr6:33754751-33754801	HRCEpiC	kidney:	n/a
20	chr6:33754751-33754801	Hepatocyte	liver:	n/a
21	chr6:33754751-33754801	AG09309	skin:	n/a
22	chr6:33754751-33754801	SK-N-SH	brain:	n/a
23	chr6:33754751-33754801	PrEC	prostate:	n/a
24	chr6:33754751-33754801	LNCaP	prostate:	n/a
25	chr6:33754751-33754801	HEK293	kidney:	embryo
26	chr6:33754751-33754801	H1-hESC	embryonic stem cell:	embryo
27	chr6:33754751-33754801	SK-N-SH_RA	brain:	n/a
28	chr6:33754751-33754801	HRPEpiC	eye:	n/a
29	chr6:33754751-33754801	RPTEC	kidney:	n/a
30	chr6:33754751-33754801	HUVEC	blood vessel:	n/a
31	chr6:33754751-33754801	HRE	kidney:	n/a
32	chr6:33754751-33754801	MCF-7	breast:	n/a
33	chr6:33754751-33754801	ECC-1	luminal epithelium:	n/a
34	chr6:33754751-33754801	PANC-1	pancreas:	n/a
35	chr6:33754751-33754801	ProgFib	skin:	n/a
36	chr6:33754751-33754801	NT2-D1	testis:	n/a
37	chr6:33754751-33754801	ovcar-3	ovarian:	n/a
38	chr6:33754751-33754801	AG10803	skin:	n/a
39	chr6:33754751-33754801	HCT-116	colon:	n/a
40	chr6:33754751-33754801	Caco-2	colon:	n/a
41	chr6:33754751-33754801	Jurkat	blood:	n/a
42	chr6:33754751-33754801	SAEC	small airway:	n/a
43	chr6:33754751-33754801	HIPEpiC	eye:	n/a
44	chr6:33754751-33754801	NHDF-neo	bronchial:	n/a
45	chr6:33754751-33754801	IMR90	lung:	fetal
46	chr6:33754751-33754801	AoSMC	blood vessel:	n/a
47	chr6:33754751-33754801	K562	blood:	n/a
48	chr6:33754751-33754801	PFSK-1	brain:	n/a
49	chr6:33754751-33754801	GM12891	blood:	n/a
50	chr6:33754751-33754801	MCF10A-Er-Src	breast:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33677771..33685795-chr6:33753004..33758704,10	MCF-7	breast:
2	chr6:33743776..33747465-chr6:33751783..33755243,5	MCF-7	breast:

No data

Variant related genes	Relation type
LEMD2	TF binding region
LEMD2	CpG island
ENSG00000137288	Chromatin interaction
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	esv3436027	chr6:33754374-33758772	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 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	chr6:33746600-33755000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:33750400-33755000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:33751600-33755200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:33752000-33755000	Genic enhancers	Brain Cingulate Gyrus	brain
5	chr6:33752400-33754800	Genic enhancers	Stomach Smooth Muscle	stomach
6	chr6:33752600-33755000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:33752600-33755200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:33752600-33755600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:33752800-33754800	Genic enhancers	Osteobl	bone
10	chr6:33752800-33755200	Genic enhancers	Brain Hippocampus Middle	brain
11	chr6:33752800-33755400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:33752800-33755400	Genic enhancers	Fetal Muscle Leg	muscle
13	chr6:33752800-33755400	Genic enhancers	Placenta	Placenta
14	chr6:33753000-33754800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:33753000-33754800	Genic enhancers	Brain Substantia Nigra	brain
16	chr6:33753000-33754800	Genic enhancers	Fetal Lung	lung
17	chr6:33753000-33755200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:33753000-33755200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:33753000-33755200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:33753000-33755200	Genic enhancers	HSMM	muscle
21	chr6:33753000-33755400	Genic enhancers	Primary B cells from peripheral blood	blood
22	chr6:33753000-33756000	Flanking Active TSS	HUVEC	blood vessel
23	chr6:33753200-33754800	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr6:33753200-33754800	Enhancers	Hela-S3	cervix
25	chr6:33753200-33755200	Genic enhancers	Fetal Stomach	stomach
26	chr6:33753200-33755200	Genic enhancers	Thymus	Thymus
27	chr6:33753200-33755400	Enhancers	Fetal Heart	heart
28	chr6:33753200-33755400	Enhancers	Right Ventricle	heart
29	chr6:33753200-33755600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr6:33753400-33755000	Weak transcription	Gastric	stomach
31	chr6:33753400-33755000	Genic enhancers	A549	lung
32	chr6:33753400-33755200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:33753400-33755200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:33753400-33755200	Weak transcription	Esophagus	oesophagus
35	chr6:33753400-33755400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr6:33753400-33755600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr6:33753400-33755800	Enhancers	Spleen	Spleen
38	chr6:33753600-33754800	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr6:33753600-33754800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
40	chr6:33753600-33754800	Genic enhancers	Monocytes-CD14+_RO01746	blood
41	chr6:33753600-33754800	Genic enhancers	NHEK	skin
42	chr6:33753600-33754800	Enhancers	NHLF	lung
43	chr6:33753600-33755000	Genic enhancers	Primary monocytes fromperipheralblood	blood
44	chr6:33753600-33755200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:33753600-33755200	Genic enhancers	Brain Angular Gyrus	brain
46	chr6:33753600-33755200	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr6:33753600-33755200	Enhancers	HSMMtube	muscle
48	chr6:33753600-33755400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:33753600-33755400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr6:33753600-33755400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links