Variant report

Variant	rs17026003
Chromosome Location	chr2:40661457-40661458
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr2:40660718-40662820	SK-N-SH	brain:	n/a	n/a
2	JUND	chr2:40660723-40662766	SK-N-SH	brain:	n/a	chr2:40661917-40661928 chr2:40662176-40662184
3	PBX3	chr2:40660703-40661485	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr2:40660758-40662717	SK-N-SH	brain:	n/a	chr2:40661679-40661688 chr2:40661681-40661688 chr2:40661679-40661689 chr2:40661674-40661695 chr2:40661681-40661688 chr2:40661676-40661692 chr2:40661681-40661688
5	GATA3	chr2:40660666-40662796	SK-N-SH	brain:	n/a	chr2:40661679-40661688 chr2:40661681-40661688 chr2:40662764-40662774 chr2:40661679-40661689 chr2:40661674-40661695 chr2:40661681-40661688 chr2:40661676-40661692 chr2:40661681-40661688

Variant related genes	Relation type
SLC8A1	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12999886	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13031545	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13031785	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13031843	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13031849	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13035085	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17025999	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17026001	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17026005	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17026009	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17026011	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17026012	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17026014	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17026018	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34038561	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34682370	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35321042	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35478019	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35797248	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35923316	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4993292	0.95[ASN][1000 genomes]
rs57193459	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61629255	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71439297	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71439298	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71439299	0.87[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	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr2:40646600-40670800	Weak transcription	Fetal Brain Female	brain
2	chr2:40647600-40662200	Weak transcription	Brain Germinal Matrix	brain
3	chr2:40648000-40667200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:40648200-40676400	Weak transcription	Fetal Kidney	kidney
5	chr2:40653000-40674800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:40654200-40662200	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:40655000-40665000	Weak transcription	Fetal Brain Male	brain
8	chr2:40657000-40671200	Weak transcription	Fetal Stomach	stomach
9	chr2:40657200-40662000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:40657800-40663000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:40657800-40666600	Enhancers	Colon Smooth Muscle	Colon
12	chr2:40658000-40663600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:40658000-40664000	Enhancers	NHDF-Ad	bronchial
14	chr2:40658000-40664200	Enhancers	HMEC	breast
15	chr2:40658200-40661800	Enhancers	HSMMtube	muscle
16	chr2:40658200-40662200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:40658200-40663400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:40658200-40663600	Enhancers	Osteobl	bone
19	chr2:40658200-40665400	Enhancers	NHLF	lung
20	chr2:40658400-40663600	Enhancers	Adipose Nuclei	Adipose
21	chr2:40658600-40661800	Enhancers	NHEK	skin
22	chr2:40658600-40663400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:40658600-40663800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:40658800-40662000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:40658800-40662800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:40659000-40662200	Weak transcription	Ovary	ovary
27	chr2:40659200-40661600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:40659200-40661600	Enhancers	Muscle Satellite Cultured Cells	--
29	chr2:40659200-40662000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr2:40659200-40662000	Weak transcription	Brain Anterior Caudate	brain
31	chr2:40659200-40663400	Enhancers	Hela-S3	cervix
32	chr2:40659600-40663200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:40659800-40662000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:40659800-40662000	Weak transcription	Right Atrium	heart
35	chr2:40659800-40664000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:40659800-40665600	Weak transcription	Dnd41	blood
37	chr2:40660000-40662000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr2:40660000-40663200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:40660200-40663400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:40660200-40663400	Enhancers	HSMM	muscle
41	chr2:40660400-40661800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:40660600-40661800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr2:40660600-40663800	Enhancers	HUVEC	blood vessel
44	chr2:40660800-40661600	Genic enhancers	Fetal Heart	heart
45	chr2:40660800-40662200	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr2:40660800-40663600	Enhancers	Aorta	Aorta
47	chr2:40660800-40664600	Enhancers	Left Ventricle	heart
48	chr2:40661000-40662000	Enhancers	NH-A	brain
49	chr2:40661000-40662200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:40661000-40664600	Enhancers	Primary monocytes fromperipheralblood	blood

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