Variant report

Variant	rs541393932
Chromosome Location	chr1:95007249-95007250
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	CTCF	chr1:95007160-95007310	HRE	kidney:	n/a	n/a
2	CHD2	chr1:95007122-95007258	HepG2	liver:	n/a	n/a
3	CTCF	chr1:95007100-95007250	AG04449	skin:	n/a	n/a
4	POLR2A	chr1:95005611-95008251	Hela-S3	cervix:	n/a	n/a
5	FOSL1	chr1:95006931-95008022	HCT-116	colon:	n/a	chr1:95007517-95007527 chr1:95007516-95007528 chr1:95007518-95007527 chr1:95007517-95007526 chr1:95007518-95007525
6	MAZ	chr1:95006679-95007730	HepG2	liver:	n/a	chr1:95006717-95006724 chr1:95006812-95006821
7	ELK1	chr1:95007183-95007253	Hela-S3	cervix:	n/a	n/a
8	FOSL1	chr1:95007030-95007921	HCT-116	colon:	n/a	chr1:95007517-95007527 chr1:95007516-95007528 chr1:95007518-95007527 chr1:95007517-95007526 chr1:95007518-95007525
9	CTCF	chr1:95007120-95007270	BJ	skin:	n/a	n/a
10	CTCF	chr1:95007200-95007350	HAc	cerebellar:	n/a	n/a
11	EGR1	chr1:95007050-95007924	HCT-116	colon:	n/a	chr1:95007475-95007485 chr1:95007384-95007398 chr1:95007410-95007424 chr1:95007477-95007490
12	GTF2F1	chr1:95007247-95008830	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr1:95007160-95007310	HCM	heart:	n/a	n/a
14	MAX	chr1:95006515-95007722	ECC-1	luminal epithelium:	n/a	chr1:95006717-95006724 chr1:95006812-95006821
15	YY1	chr1:95006746-95007703	HepG2	liver:	n/a	chr1:95007468-95007479 chr1:95006869-95006880
16	MAZ	chr1:95006424-95007855	Hela-S3	cervix:	n/a	chr1:95006717-95006724 chr1:95006812-95006821
17	RAD21	chr1:95007068-95007716	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:95007031-95007714	Gliobla	brain:	n/a	n/a
19	CTCF	chr1:95007100-95007250	HPF	lung:	n/a	n/a
20	CTCF	chr1:95007100-95007250	GM12871	blood:	n/a	n/a
21	CTCF	chr1:95007113-95007281	Fibrobl	skin:	n/a	n/a
22	TAF1	chr1:95006872-95007705	HepG2	liver:	n/a	n/a
23	TBP	chr1:95007141-95007710	Hela-S3	cervix:	n/a	n/a
24	CHD2	chr1:95006578-95007853	Hela-S3	cervix:	n/a	n/a
25	TCF12	chr1:95006785-95007899	ECC-1	luminal epithelium:	n/a	n/a
26	CTCF	chr1:95007135-95007256	MCF-7	breast:	n/a	n/a
27	JUND	chr1:95007204-95007326	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr1:95007200-95007350	NHDF-neo	bronchial:	n/a	n/a
29	CTCF	chr1:95007140-95007290	HepG2	liver:	n/a	n/a
30	BACH1	chr1:95006990-95008182	H1-hESC	embryonic stem cell:	n/a	chr1:95007515-95007529
31	POLR2A	chr1:95006964-95007899	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr1:95006048-95007983	Hela-S3	cervix:	n/a	n/a
33	EGR1	chr1:95007172-95007632	K562	blood:	n/a	chr1:95007475-95007485 chr1:95007384-95007398 chr1:95007410-95007424 chr1:95007477-95007490
34	POLR2A	chr1:95006942-95007764	HEK293	kidney:	n/a	n/a
35	POLR2A	chr1:94991604-95010849	IMR90	lung:	n/a	n/a
36	EP300	chr1:95007224-95008277	SK-N-SH	brain:	n/a	chr1:95007518-95007527 chr1:95008212-95008226 chr1:95008206-95008220
37	CTCF	chr1:95007140-95007290	AG10803	skin:	n/a	n/a
38	HA-E2F1	chr1:95006261-95007853	MCF-7	breast:	n/a	chr1:95007476-95007485
39	POLR2A	chr1:95006117-95008373	Hela-S3	cervix:	n/a	n/a
40	HEY1	chr1:95007069-95007773	HepG2	liver:	n/a	chr1:95007318-95007333 chr1:95007545-95007560
41	CTCF	chr1:95007180-95007330	WI-38	lung:	n/a	n/a
42	JUN	chr1:95007199-95007869	K562	blood:	n/a	chr1:95007517-95007527 chr1:95007516-95007528 chr1:95007518-95007527 chr1:95007517-95007526 chr1:95007518-95007525
43	POLR2A	chr1:95000323-95009541	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr1:95006847-95007732	ECC-1	luminal epithelium:	n/a	n/a
45	SMARCB1	chr1:95006190-95008144	Hela-S3	cervix:	n/a	chr1:95007517-95007526 chr1:95007518-95007527
46	RAD21	chr1:95007150-95007256	HepG2	liver:	n/a	n/a
47	POLR2A	chr1:95006887-95008137	A549	lung:	n/a	n/a
48	POLR2A	chr1:95007004-95007390	HCT-116	colon:	n/a	n/a
49	POLR2A	chr1:95003836-95008278	U87	brain:	n/a	n/a
50	RCOR1	chr1:95006244-95008216	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:95001173..95003691-chr1:95006398..95009153,2	MCF-7	breast:
2	chr1:95006856..95007717-chr15:75932354..75933289,2	NB4	blood:

Variant related genes	Relation type
F3	TF binding region
ENSG00000177971	Chromatin interaction
ENSG00000117525	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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	nsv531881	chr1:94937444-95053785	Weak transcription Bivalent Enhancer Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv870696	chr1:95005220-95081587	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv871391	chr1:95005220-95083836	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv3437143	chr1:95006189-95008737	Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95001600-95007400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:95001600-95007800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:95001800-95007800	Active TSS	Brain Hippocampus Middle	brain
4	chr1:95002800-95007600	Active TSS	Brain Anterior Caudate	brain
5	chr1:95003000-95007800	Active TSS	Right Atrium	heart
6	chr1:95003000-95008400	Active TSS	Brain Angular Gyrus	brain
7	chr1:95003200-95007800	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr1:95003200-95007800	Active TSS	Fetal Intestine Large	intestine
9	chr1:95003800-95007600	Active TSS	Stomach Smooth Muscle	stomach
10	chr1:95003800-95007800	Active TSS	Brain Cingulate Gyrus	brain
11	chr1:95004200-95008800	Active TSS	Ovary	ovary
12	chr1:95004400-95007800	Active TSS	Left Ventricle	heart
13	chr1:95004400-95007800	Active TSS	Right Ventricle	heart
14	chr1:95004400-95007800	Active TSS	NH-A	brain
15	chr1:95004400-95008200	Active TSS	Pancreas	Pancrea
16	chr1:95004600-95007800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:95004800-95007800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:95004800-95007800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:95005400-95007600	Active TSS	Duodenum Mucosa	Duodenum
20	chr1:95005400-95007800	Active TSS	HSMMtube	muscle
21	chr1:95005400-95008000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
22	chr1:95005400-95008000	Active TSS	Placenta Amnion	Placenta Amnion
23	chr1:95005400-95008000	Active TSS	Stomach Mucosa	stomach
24	chr1:95005400-95008400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr1:95005600-95007800	Active TSS	Fetal Heart	heart
26	chr1:95005600-95008200	Active TSS	NHDF-Ad	bronchial
27	chr1:95005600-95008800	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr1:95005800-95008000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
29	chr1:95005800-95008000	Active TSS	Brain Substantia Nigra	brain
30	chr1:95005800-95008200	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr1:95005800-95008600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:95006000-95007600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:95006000-95007600	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
34	chr1:95006000-95007600	Active TSS	Hela-S3	cervix
35	chr1:95006000-95007800	Active TSS	Rectal Smooth Muscle	rectum
36	chr1:95006200-95007600	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr1:95006200-95007800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:95006200-95007800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:95006200-95007800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:95006200-95007800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:95006200-95007800	Active TSS	Colonic Mucosa	Colon
42	chr1:95006200-95007800	Bivalent/Poised TSS	Fetal Stomach	stomach
43	chr1:95006200-95008000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
44	chr1:95006200-95008200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:95006200-95008600	Active TSS	Aorta	Aorta
46	chr1:95006400-95007600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
47	chr1:95006400-95007800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:95006400-95007800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:95006400-95007800	Active TSS	Small Intestine	intestine
50	chr1:95006400-95008000	Active TSS	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links