Variant report

Variant	rs12126296
Chromosome Location	chr1:161991193-161991194
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	chr1:161989258..161991462-chr1:161992254..161993914,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162745	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12119861	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12120969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12125293	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12130792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57311038	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv464206	chr1:161798239-162067447	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv470744	chr1:161798239-162067447	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv548077	chr1:161798239-162067447	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1007108	chr1:161925814-162002917	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv831747	chr1:161926367-162103311	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161979200-161993200	Weak transcription	Gastric	stomach
2	chr1:161986800-161993000	Weak transcription	Spleen	Spleen
3	chr1:161988000-161992400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:161988200-161991200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr1:161988200-161991200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:161988200-161991200	Enhancers	Left Ventricle	heart
7	chr1:161988400-161991200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:161988400-161991200	Enhancers	Right Ventricle	heart
9	chr1:161988400-161991200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr1:161988600-161991800	Enhancers	NHLF	lung
11	chr1:161989400-161991200	Weak transcription	Placenta	Placenta
12	chr1:161989400-161992400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:161989400-161993000	Weak transcription	HUVEC	blood vessel
14	chr1:161989600-161991400	Weak transcription	NH-A	brain
15	chr1:161989600-161991800	Weak transcription	Brain Angular Gyrus	brain
16	chr1:161989600-161992000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:161989600-161992400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:161989600-161992600	Weak transcription	Ovary	ovary
19	chr1:161989600-161993000	Weak transcription	Brain Substantia Nigra	brain
20	chr1:161989800-161992600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:161989800-161992600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:161989800-161993000	Weak transcription	Pancreas	Pancrea
23	chr1:161990000-161992400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:161990000-161992600	Weak transcription	Brain Anterior Caudate	brain
25	chr1:161990000-161993000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:161990200-161992600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:161990400-161992000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:161990400-161992000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:161990600-161991200	Enhancers	Rectal Smooth Muscle	rectum
30	chr1:161990600-161991400	Enhancers	Right Atrium	heart
31	chr1:161990600-161992000	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr1:161990800-161991200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
33	chr1:161990800-161991200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:161990800-161991200	Enhancers	Lung	lung
35	chr1:161990800-161991400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr1:161990800-161991400	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr1:161990800-161991400	Flanking Active TSS	Fetal Muscle Trunk	muscle
38	chr1:161990800-161991600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:161990800-161991600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr1:161990800-161991600	Enhancers	Colon Smooth Muscle	Colon
41	chr1:161990800-161991600	Flanking Active TSS	NHDF-Ad	bronchial
42	chr1:161990800-161991800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:161990800-161991800	Bivalent Enhancer	Fetal Stomach	stomach
44	chr1:161990800-161992000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:161990800-161992000	Flanking Active TSS	Fetal Muscle Leg	muscle
46	chr1:161990800-161992000	Flanking Active TSS	HSMMtube	muscle
47	chr1:161990800-161992400	Enhancers	H1 Cell Line	embryonic stem cell
48	chr1:161991000-161991200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:161991000-161991200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:161991000-161991200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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