Variant report

Variant	rs3006989
Chromosome Location	chr1:114527523-114527524
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114525379..114527622-chr1:114550008..114552290,2	MCF-7	breast:
2	chr1:114526776..114528757-chr20:45985728..45987939,2	MCF-7	breast:
3	chr1:114527463..114529222-chr1:114530804..114533852,3	MCF-7	breast:
4	chr1:114525871..114528123-chr1:114528242..114530523,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11102712	0.87[ASN][1000 genomes]
rs1158910	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1158911	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158912	0.91[ASN][1000 genomes]
rs12029644	0.87[ASN][1000 genomes]
rs1354373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17032048	0.91[ASN][1000 genomes]
rs1806736	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1806763	0.89[ASN][1000 genomes]
rs2358997	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2358998	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2884604	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2938319	0.89[ASN][1000 genomes]
rs2938320	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3006981	0.89[ASN][1000 genomes]
rs3006988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006996	0.89[ASN][1000 genomes]
rs3006998	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3006999	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3007002	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7520320	0.87[ASN][1000 genomes]
rs924778	0.90[ASN][1000 genomes]
rs937672	0.89[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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114523800-114534600	Weak transcription	Primary T cells from cord blood	blood
2	chr1:114524000-114527800	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr1:114524400-114528000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:114524800-114527600	Enhancers	Fetal Thymus	thymus
5	chr1:114524800-114528000	Flanking Active TSS	Fetal Muscle Leg	muscle
6	chr1:114525000-114527600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:114525000-114528000	Enhancers	Lung	lung
8	chr1:114525200-114527800	Enhancers	Thymus	Thymus
9	chr1:114525600-114527800	Enhancers	Brain Hippocampus Middle	brain
10	chr1:114525600-114528000	Enhancers	Left Ventricle	heart
11	chr1:114525600-114528000	Enhancers	Right Atrium	heart
12	chr1:114525600-114528200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:114525800-114527800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:114525800-114528000	Enhancers	Ovary	ovary
15	chr1:114526000-114527600	Enhancers	Osteobl	bone
16	chr1:114526000-114527800	Enhancers	Fetal Intestine Small	intestine
17	chr1:114526000-114528000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:114526200-114529600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:114526400-114527600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:114526400-114527600	Weak transcription	Fetal Intestine Large	intestine
21	chr1:114526400-114527600	Enhancers	Placenta	Placenta
22	chr1:114526400-114527600	Weak transcription	Spleen	Spleen
23	chr1:114526400-114527600	Flanking Active TSS	HSMMtube	muscle
24	chr1:114526400-114527800	Enhancers	Colonic Mucosa	Colon
25	chr1:114526400-114528000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:114526400-114528000	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr1:114526600-114527600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:114526600-114527600	Weak transcription	Psoas Muscle	Psoas
29	chr1:114526600-114527600	Enhancers	HSMM	muscle
30	chr1:114526600-114527800	Enhancers	Adipose Nuclei	Adipose
31	chr1:114526600-114527800	Enhancers	NHDF-Ad	bronchial
32	chr1:114526600-114529400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:114526800-114527600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:114526800-114527800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:114526800-114527800	Enhancers	Fetal Kidney	kidney
36	chr1:114526800-114528000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:114526800-114528000	Enhancers	Rectal Smooth Muscle	rectum
38	chr1:114526800-114528400	Genic enhancers	Fetal Stomach	stomach
39	chr1:114527000-114527600	Enhancers	Fetal Lung	lung
40	chr1:114527000-114527600	Weak transcription	HepG2	liver
41	chr1:114527000-114527800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr1:114527000-114527800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:114527000-114527800	Enhancers	NH-A	brain
44	chr1:114527000-114528400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
45	chr1:114527200-114527600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:114527200-114527800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:114527200-114527800	Enhancers	Primary hematopoietic stem cells	blood
48	chr1:114527200-114528000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
49	chr1:114527200-114528000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:114527200-114528000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links