Variant report

Variant	rs3789685
Chromosome Location	chr1:95004938-95004939
allele	C/T
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	chr1:95004816-95005515	Hela-S3	cervix:	n/a	n/a
2	FOS	chr1:95004708-95005855	MCF10A-Er-Src	breast:	n/a	chr1:95005291-95005301
3	POLR2A	chr1:94992567-95005960	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:94991604-95010849	IMR90	lung:	n/a	n/a
5	POLR2A	chr1:95000323-95009541	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:95003836-95008278	U87	brain:	n/a	n/a
7	CHD1	chr1:94994939-95011321	IMR90	lung:	n/a	n/a
8	POLR2A	chr1:95004799-95008370	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:95004630-95008333	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr1:95004930-95005865	MCF10A-Er-Src	breast:	n/a	chr1:95005291-95005301
11	POLR2A	chr1:95003842-95005922	U87	brain:	n/a	n/a
12	POLR2A	chr1:94999692-95008368	ProgFib	skin:	n/a	n/a
13	MAZ	chr1:95004703-95008397	IMR90	lung:	n/a	chr1:95006717-95006724 chr1:95006812-95006821

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:95004605..95005274-chr18:74502570..74503410,2	MCF-7	breast:
2	chr1:95004121..95007110-chr1:95017554..95021316,3	MCF-7	breast:

Variant related genes	Relation type
F3	TF binding region

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

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1028736	1.00[ASN][1000 genomes]
rs3917608	1.00[ASN][1000 genomes]
rs72968370	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94965600-95006400	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:94979200-95005000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:94986000-95006200	Weak transcription	Liver	Liver
4	chr1:94994400-95005400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:94994600-95005200	Weak transcription	Esophagus	oesophagus
6	chr1:94994600-95006200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:94995200-95006200	Weak transcription	Spleen	Spleen
8	chr1:94996800-95005200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:94997600-95005000	Weak transcription	Dnd41	blood
10	chr1:94997600-95005200	Weak transcription	Gastric	stomach
11	chr1:94999000-95005400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr1:95000400-95005600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
13	chr1:95001200-95006400	Weak transcription	Small Intestine	intestine
14	chr1:95001400-95006600	Transcr. at gene 5' and 3'	HMEC	breast
15	chr1:95001600-95006200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:95001600-95007400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:95001600-95007800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:95001800-95006000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:95001800-95006200	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr1:95001800-95007000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:95001800-95007800	Active TSS	Brain Hippocampus Middle	brain
22	chr1:95002000-95005000	Weak transcription	Fetal Stomach	stomach
23	chr1:95002000-95005400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:95002000-95006200	Weak transcription	Aorta	Aorta
25	chr1:95002200-95005200	Weak transcription	Fetal Muscle Leg	muscle
26	chr1:95002200-95006000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:95002400-95006600	Transcr. at gene 5' and 3'	NHLF	lung
28	chr1:95002600-95005800	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:95002600-95006600	Active TSS	Fetal Brain Female	brain
30	chr1:95002800-95005400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:95002800-95005800	Enhancers	Fetal Brain Male	brain
32	chr1:95002800-95006800	Transcr. at gene 5' and 3'	NHEK	skin
33	chr1:95002800-95007200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:95002800-95007600	Active TSS	Brain Anterior Caudate	brain
35	chr1:95003000-95007800	Active TSS	Right Atrium	heart
36	chr1:95003000-95008400	Active TSS	Brain Angular Gyrus	brain
37	chr1:95003200-95006400	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr1:95003200-95007800	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr1:95003200-95007800	Active TSS	Fetal Intestine Large	intestine
40	chr1:95003400-95005200	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
41	chr1:95003400-95005200	Flanking Active TSS	Fetal Heart	heart
42	chr1:95003600-95005200	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr1:95003800-95005000	Active TSS	Brain Substantia Nigra	brain
44	chr1:95003800-95007600	Active TSS	Stomach Smooth Muscle	stomach
45	chr1:95003800-95007800	Active TSS	Brain Cingulate Gyrus	brain
46	chr1:95004000-95005000	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr1:95004000-95005000	Genic enhancers	HSMM	muscle
48	chr1:95004000-95005200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
49	chr1:95004000-95005400	Active TSS	Colonic Mucosa	Colon
50	chr1:95004000-95005600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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