Variant report

Variant	rs12090310
Chromosome Location	chr1:94766435-94766436
allele	A/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	chr1:94765226-94767241	HCT-116	colon:	n/a	n/a
2	SP1	chr1:94765032-94767451	HCT-116	colon:	n/a	chr1:94765317-94765329 chr1:94765318-94765327
3	FOSL1	chr1:94765319-94766483	HCT-116	colon:	n/a	n/a
4	CEBPB	chr1:94765288-94767446	HCT-116	colon:	n/a	n/a
5	MAX	chr1:94765086-94766438	HCT-116	colon:	n/a	n/a
6	SP1	chr1:94765421-94766437	HCT-116	colon:	n/a	n/a
7	FOSL1	chr1:94765149-94767364	HCT-116	colon:	n/a	chr1:94767015-94767023
8	POLR2A	chr1:94765261-94767058	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
GAPDHP29	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11165098	0.89[ASN][1000 genomes]
rs11165104	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11165105	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11165111	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11587699	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069420	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12084043	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12090491	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12096115	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1330855	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1687949	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17111360	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1756254	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2150269	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2774923	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28613199	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35493159	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3789688	0.88[ASN][1000 genomes]
rs3814019	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3827751	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs58466782	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59960594	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs722296	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7525008	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7528831	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7530160	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7538484	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7540684	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7548951	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	nsv428510	chr1:94709575-94866655	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94760600-94770000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:94761200-94767000	Enhancers	NHLF	lung
3	chr1:94761200-94767400	Enhancers	Muscle Satellite Cultured Cells	--
4	chr1:94761200-94768200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:94762000-94769400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr1:94762200-94767200	Enhancers	HepG2	liver
7	chr1:94763400-94767200	Weak transcription	Right Ventricle	heart
8	chr1:94763400-94775800	Weak transcription	Psoas Muscle	Psoas
9	chr1:94764200-94767200	Enhancers	Liver	Liver
10	chr1:94764200-94767200	Enhancers	Osteobl	bone
11	chr1:94764400-94766600	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr1:94764400-94767200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:94764400-94767400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:94764400-94767800	Enhancers	HMEC	breast
15	chr1:94764400-94767800	Enhancers	NHDF-Ad	bronchial
16	chr1:94764600-94767200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr1:94764600-94767200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr1:94764800-94766800	Enhancers	Fetal Intestine Small	intestine
19	chr1:94764800-94767600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:94764800-94771200	Enhancers	HUVEC	blood vessel
21	chr1:94764800-94772000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:94765000-94767400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:94765000-94768600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:94765200-94766600	Enhancers	Small Intestine	intestine
25	chr1:94765200-94766800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr1:94765200-94767200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr1:94765200-94767200	Enhancers	Right Atrium	heart
28	chr1:94765200-94767200	Enhancers	NH-A	brain
29	chr1:94765200-94767400	Enhancers	Placenta Amnion	Placenta Amnion
30	chr1:94765200-94768800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:94765400-94767200	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr1:94765400-94767800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr1:94765600-94767200	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr1:94765600-94768000	Weak transcription	Ovary	ovary
35	chr1:94765800-94766600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:94765800-94766800	Weak transcription	Primary B cells from cord blood	blood
37	chr1:94765800-94767000	Weak transcription	Left Ventricle	heart
38	chr1:94765800-94767000	Weak transcription	Lung	lung
39	chr1:94765800-94768000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:94765800-94768000	Weak transcription	Pancreas	Pancrea
41	chr1:94765800-94768200	Weak transcription	Gastric	stomach
42	chr1:94765800-94768600	Enhancers	Adipose Nuclei	Adipose
43	chr1:94765800-94769200	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr1:94765800-94770800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:94766000-94767000	Weak transcription	Spleen	Spleen
46	chr1:94766000-94767400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:94766000-94767400	Enhancers	Hela-S3	cervix
48	chr1:94766000-94767400	Enhancers	NHEK	skin
49	chr1:94766000-94768200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:94766000-94770000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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