Variant report

Variant	rs9819129
Chromosome Location	chr3:112989763-112989764
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112986625..112989851-chr3:112997054..112999009,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144857	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10511324	0.90[EUR][1000 genomes]
rs13326562	0.81[EUR][1000 genomes]
rs1499898	0.91[AFR][1000 genomes]
rs16860720	0.91[AFR][1000 genomes]
rs16860734	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28679287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3995908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6438134	0.95[EUR][1000 genomes]
rs7652801	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9288980	0.90[EUR][1000 genomes]
rs9811168	0.81[EUR][1000 genomes]
rs9820139	0.91[AFR][1000 genomes]
rs9820627	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9823770	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831049	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831364	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831793	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9832953	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs9836199	0.81[EUR][1000 genomes]
rs9837357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9840485	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9851183	0.81[EUR][1000 genomes]
rs9853439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9863114	0.81[EUR][1000 genomes]
rs9864630	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9872998	0.83[AFR][1000 genomes]

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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112969000-112995200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:112969800-112991800	Weak transcription	Right Ventricle	heart
3	chr3:112969800-112994200	Weak transcription	Spleen	Spleen
4	chr3:112973600-112993000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
6	chr3:112974200-112994600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:112978600-112991400	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:112981200-112991000	Genic enhancers	Fetal Muscle Leg	muscle
9	chr3:112981400-112989800	Weak transcription	Gastric	stomach
10	chr3:112981600-112994400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:112982000-112989800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:112982800-112993600	Weak transcription	HMEC	breast
13	chr3:112983800-112995000	Weak transcription	Lung	lung
14	chr3:112984000-112994400	Weak transcription	HSMMtube	muscle
15	chr3:112984200-112989800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:112984200-112993600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:112984200-112994400	Weak transcription	HSMM	muscle
18	chr3:112984600-112989800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:112984600-112991200	Weak transcription	Brain Germinal Matrix	brain
20	chr3:112984600-112993400	Weak transcription	Fetal Brain Male	brain
21	chr3:112984800-112992400	Weak transcription	Fetal Thymus	thymus
22	chr3:112984800-112993000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr3:112984800-112998400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:112985400-112990000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:112985400-112993600	Strong transcription	Fetal Lung	lung
27	chr3:112986200-112990400	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr3:112986200-112994200	Strong transcription	Ovary	ovary
29	chr3:112986400-112993000	Strong transcription	Fetal Intestine Small	intestine
30	chr3:112986400-112994600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:112986600-112990600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:112986600-112993800	Weak transcription	Brain Substantia Nigra	brain
33	chr3:112987200-112990600	Strong transcription	Fetal Intestine Large	intestine
34	chr3:112987200-112993400	Strong transcription	Fetal Stomach	stomach
35	chr3:112987200-112994400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:112987400-112991200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:112987800-112990000	Strong transcription	Stomach Smooth Muscle	stomach
38	chr3:112987800-112991200	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:112987800-112996000	Enhancers	Pancreas	Pancrea
40	chr3:112988000-112990200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:112988000-112991000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr3:112988000-112992200	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:112988000-112993600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:112988000-112993800	Weak transcription	Brain Angular Gyrus	brain
45	chr3:112988000-113003000	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr3:112988200-112992600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:112988200-112993400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:112988200-112993600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:112988200-112993800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:112988200-112994200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links