Variant report

Variant	rs7519939
Chromosome Location	chr1:94058281-94058282
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	POLR2A	chr1:94058174-94058381	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:94057137-94058481	PFSK-1	brain:	n/a	n/a
3	MBD4	chr1:94057120-94058544	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:94057236-94058879	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:94057671-94058392	Hela-S3	cervix:	n/a	n/a
6	TBP	chr1:94057166-94058528	HepG2	liver:	n/a	n/a
7	HEY1	chr1:94056860-94058945	HepG2	liver:	n/a	n/a
8	MXI1	chr1:94058049-94059051	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr1:94057281-94058420	HepG2	liver:	n/a	n/a
10	MXI1	chr1:94057054-94058396	HepG2	liver:	n/a	chr1:94057400-94057409
11	REST	chr1:94058138-94058936	PFSK-1	brain:	n/a	chr1:94058669-94058682
12	MAX	chr1:94057088-94058422	HepG2	liver:	n/a	chr1:94057611-94057621
13	BHLHE40	chr1:94057253-94058342	HepG2	liver:	n/a	n/a
14	POLR2A	chr1:94057261-94058412	HepG2	liver:	n/a	n/a
15	MAX	chr1:94056964-94059251	HepG2	liver:	n/a	chr1:94057611-94057621
16	POLR2A	chr1:94057268-94058904	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:94057079-94058772	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:94057261-94058811	Hela-S3	cervix:	n/a	n/a
19	TCF12	chr1:94057245-94058338	ECC-1	luminal epithelium:	n/a	chr1:94057476-94057483 chr1:94057400-94057410
20	MAX	chr1:94057000-94058505	HepG2	liver:	n/a	chr1:94057611-94057621
21	POLR2A	chr1:94057229-94058804	HepG2	liver:	n/a	n/a
22	POLR2A	chr1:94057179-94058869	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000224093	TF binding region
BCAR3	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs17110124	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1772781	0.83[EUR][1000 genomes]
rs1772782	0.85[EUR][1000 genomes]
rs2281474	0.95[ASN][1000 genomes]
rs236313	0.83[EUR][1000 genomes]
rs236322	0.95[ASN][1000 genomes]
rs236323	0.95[ASN][1000 genomes]
rs236326	0.95[ASN][1000 genomes]
rs236329	0.98[ASN][1000 genomes]
rs236330	0.97[ASN][1000 genomes]
rs236331	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236332	0.97[ASN][1000 genomes]
rs236333	0.97[ASN][1000 genomes]
rs236335	0.92[ASN][1000 genomes]
rs3767973	0.94[ASN][1000 genomes]
rs3767975	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3767976	0.94[ASN][1000 genomes]
rs3767977	0.97[ASN][1000 genomes]
rs399649	0.83[EUR][1000 genomes]
rs57012808	0.95[ASN][1000 genomes]
rs57466479	0.94[ASN][1000 genomes]
rs57914444	0.94[ASN][1000 genomes]
rs59777284	0.94[ASN][1000 genomes]
rs6661488	0.95[ASN][1000 genomes]
rs6671749	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692801	0.95[ASN][1000 genomes]
rs7516400	0.95[ASN][1000 genomes]
rs7518795	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7524368	0.94[ASN][1000 genomes]
rs7551964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94025600-94073800	Weak transcription	Fetal Brain Female	brain
2	chr1:94041800-94059400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:94042200-94063200	Weak transcription	Brain Germinal Matrix	brain
4	chr1:94043000-94058400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:94048200-94059200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:94048200-94059400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:94048400-94059600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:94048600-94064200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:94049600-94059400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:94050000-94059400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:94050800-94059200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:94053600-94063000	Genic enhancers	Muscle Satellite Cultured Cells	--
13	chr1:94054200-94058400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:94054400-94061000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:94054600-94058400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr1:94054600-94062000	Weak transcription	Brain Substantia Nigra	brain
17	chr1:94055000-94059200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:94055200-94058800	Enhancers	Primary hematopoietic stem cells	blood
19	chr1:94055600-94058800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:94055800-94061000	Weak transcription	Aorta	Aorta
21	chr1:94056000-94066000	Weak transcription	Ovary	ovary
22	chr1:94056800-94060200	Enhancers	Pancreas	Pancrea
23	chr1:94057000-94058400	Flanking Active TSS	Liver	Liver
24	chr1:94057000-94058800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr1:94057000-94060200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:94057000-94060200	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr1:94057000-94060200	Genic enhancers	HMEC	breast
28	chr1:94057200-94058400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:94057200-94058400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:94057200-94058400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:94057200-94058400	Enhancers	Fetal Lung	lung
32	chr1:94057200-94058400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr1:94057200-94058600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:94057200-94059000	Flanking Active TSS	Fetal Intestine Large	intestine
35	chr1:94057200-94059000	Enhancers	Fetal Kidney	kidney
36	chr1:94057200-94060000	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr1:94057200-94060200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:94057200-94060400	Enhancers	Left Ventricle	heart
39	chr1:94057200-94060400	Enhancers	Psoas Muscle	Psoas
40	chr1:94057400-94058400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:94057400-94058400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr1:94057400-94058400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:94057400-94058400	Genic enhancers	Lung	lung
44	chr1:94057400-94058400	Enhancers	Placenta Amnion	Placenta Amnion
45	chr1:94057400-94058600	Flanking Active TSS	Stomach Mucosa	stomach
46	chr1:94057400-94059000	Flanking Active TSS	Fetal Intestine Small	intestine
47	chr1:94057400-94068000	Genic enhancers	HSMM	muscle
48	chr1:94057400-94069200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:94057400-94071000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:94057600-94058400	Active TSS	Rectal Smooth Muscle	rectum

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