Variant report

Variant	rs12632492
Chromosome Location	chr3:113232879-113232880
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:113229615..113239929-chr3:113247196..113257849,45	MCF-7	breast:
2	chr3:112279637..112281423-chr3:113232414..113235211,2	K562	blood:
3	chr3:113232695..113235446-chr3:113249011..113251267,3	K562	blood:
4	chr3:112709917..112711539-chr3:113232036..113234156,2	K562	blood:
5	chr3:113232788..113235774-chr3:113464780..113467765,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000072858	Chromatin interaction
ENSG00000242659	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000272844	Chromatin interaction
ENSG00000114573	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000121579	Chromatin interaction
ENSG00000138459	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10934229	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10934230	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10934233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054036	0.91[EUR][1000 genomes]
rs12629271	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12629498	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12630518	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12631929	0.82[EUR][1000 genomes]
rs12637924	0.85[EUR][1000 genomes]
rs1463644	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16860899	0.83[EUR][1000 genomes]
rs2271495	0.82[EUR][1000 genomes]
rs2306069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399481	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732804	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3896909	0.81[EUR][1000 genomes]
rs4682137	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4682489	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55757335	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55865352	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60292736	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62265992	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62265996	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73237104	0.85[EUR][1000 genomes]
rs73237110	0.85[EUR][1000 genomes]
rs73237123	0.85[EUR][1000 genomes]
rs73237130	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73237143	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73239107	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73239126	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7637206	0.82[EUR][1000 genomes]
rs8179926	0.85[EUR][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	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
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113176400-113233200	Weak transcription	Gastric	stomach
2	chr3:113184000-113233200	Weak transcription	Pancreas	Pancrea
3	chr3:113204600-113233200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:113204600-113233200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:113204600-113233200	Weak transcription	Esophagus	oesophagus
6	chr3:113204800-113233200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:113207600-113233000	Weak transcription	Psoas Muscle	Psoas
8	chr3:113207800-113233000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:113210000-113233000	Weak transcription	HSMM	muscle
10	chr3:113210200-113233200	Weak transcription	Colonic Mucosa	Colon
11	chr3:113217800-113233000	Weak transcription	Small Intestine	intestine
12	chr3:113225000-113233200	Weak transcription	Spleen	Spleen
13	chr3:113225200-113233000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:113225200-113233200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:113225400-113233000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr3:113225400-113233000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:113225400-113233000	Weak transcription	Fetal Thymus	thymus
18	chr3:113225400-113233200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:113225400-113233200	Weak transcription	Aorta	Aorta
20	chr3:113225400-113233200	Weak transcription	Placenta	Placenta
21	chr3:113225400-113233200	Weak transcription	Left Ventricle	heart
22	chr3:113225400-113233200	Weak transcription	Ovary	ovary
23	chr3:113232000-113233400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:113232400-113233000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:113232400-113233000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr3:113232400-113233000	Enhancers	Fetal Heart	heart
27	chr3:113232400-113233000	Enhancers	Placenta Amnion	Placenta Amnion
28	chr3:113232400-113233200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:113232400-113233200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:113232400-113233400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:113232400-113233400	Flanking Active TSS	Dnd41	blood
32	chr3:113232400-113235200	Active TSS	A549	lung
33	chr3:113232600-113233000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:113232600-113233000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:113232600-113233000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
36	chr3:113232600-113233000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:113232600-113233000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:113232600-113233000	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr3:113232600-113233000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:113232600-113233000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:113232600-113233000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:113232600-113233000	Enhancers	Brain Angular Gyrus	brain
43	chr3:113232600-113233000	Enhancers	Brain Cingulate Gyrus	brain
44	chr3:113232600-113233000	Enhancers	Brain Hippocampus Middle	brain
45	chr3:113232600-113233000	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr3:113232600-113233000	Flanking Active TSS	NHDF-Ad	bronchial
47	chr3:113232600-113233200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:113232600-113233200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr3:113232600-113233200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr3:113232600-113233400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links