Variant report

Variant	rs9879839
Chromosome Location	chr3:134124907-134124908
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:134092810..134094384-chr3:134122425..134125070,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114019	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10222468	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10433422	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2133306	0.89[EUR][1000 genomes]
rs3846051	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3913264	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4974503	0.89[EUR][1000 genomes]
rs4998531	0.95[EUR][1000 genomes]
rs6771287	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783899	0.96[EUR][1000 genomes]
rs9289470	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9829949	0.96[EUR][1000 genomes]
rs9842071	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849457	0.88[EUR][1000 genomes]
rs9853685	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9866933	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134116000-134125000	Weak transcription	Right Ventricle	heart
2	chr3:134122000-134125200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:134122400-134125000	Enhancers	HSMMtube	muscle
4	chr3:134123400-134125200	Weak transcription	Esophagus	oesophagus
5	chr3:134123800-134125000	Enhancers	Brain Hippocampus Middle	brain
6	chr3:134123800-134125000	Enhancers	Brain Substantia Nigra	brain
7	chr3:134123800-134125200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:134124000-134125200	Enhancers	Brain Cingulate Gyrus	brain
9	chr3:134124000-134125200	Weak transcription	Pancreas	Pancrea
10	chr3:134124200-134125000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
11	chr3:134124200-134125000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:134124200-134125000	Enhancers	Brain Germinal Matrix	brain
13	chr3:134124200-134125000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr3:134124400-134125000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr3:134124400-134125000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:134124400-134125000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr3:134124400-134125000	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr3:134124400-134125000	Enhancers	Ovary	ovary
19	chr3:134124400-134125200	Enhancers	Brain Angular Gyrus	brain
20	chr3:134124400-134125200	Bivalent Enhancer	Fetal Stomach	stomach
21	chr3:134124400-134125200	Enhancers	Left Ventricle	heart
22	chr3:134124400-134125200	Bivalent Enhancer	Stomach Mucosa	stomach
23	chr3:134124400-134125400	Enhancers	Gastric	stomach
24	chr3:134124400-134125400	Enhancers	Lung	lung
25	chr3:134124400-134125600	Bivalent Enhancer	Fetal Lung	lung
26	chr3:134124400-134126600	Enhancers	Fetal Brain Male	brain
27	chr3:134124600-134125000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
28	chr3:134124600-134125000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:134124600-134125000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:134124600-134125000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
31	chr3:134124600-134125000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:134124600-134125000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:134124600-134125200	Active TSS	HSMM	muscle
34	chr3:134124600-134126200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
35	chr3:134124600-134126200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr3:134124600-134126200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
37	chr3:134124800-134125000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
38	chr3:134124800-134125000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:134124800-134125000	Weak transcription	Brain Anterior Caudate	brain
40	chr3:134124800-134125800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
41	chr3:134124800-134126000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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