Variant report

Variant	rs73932787
Chromosome Location	chr2:54740439-54740440
allele	G/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	RUNX3	chr2:54740182-54740536	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54739309..54741349-chr2:54741528..54743600,2	MCF-7	breast:

Variant related genes	Relation type
SPTBN1	TF binding region
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13405115	1.00[ASN][1000 genomes]
rs17343918	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17344343	1.00[ASN][1000 genomes]
rs17415829	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17415857	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17416291	1.00[ASN][1000 genomes]
rs17521510	1.00[ASN][1000 genomes]
rs17580255	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17580855	1.00[ASN][1000 genomes]
rs17580876	1.00[ASN][1000 genomes]
rs3796015	0.83[EUR][1000 genomes]
rs41281497	1.00[ASN][1000 genomes]
rs4440005	0.83[EUR][1000 genomes]
rs57810131	1.00[ASN][1000 genomes]
rs58143357	1.00[ASN][1000 genomes]
rs59228485	1.00[ASN][1000 genomes]
rs61480394	1.00[ASN][1000 genomes]
rs72911560	1.00[ASN][1000 genomes]
rs72911563	1.00[ASN][1000 genomes]
rs72915032	1.00[ASN][1000 genomes]
rs73932786	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1002611	chr2:54718022-54752839	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr2:54719000-54751800	Weak transcription	Aorta	Aorta
2	chr2:54730400-54747600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:54732800-54754800	Weak transcription	Fetal Intestine Small	intestine
4	chr2:54733000-54743800	Weak transcription	Small Intestine	intestine
5	chr2:54733600-54747000	Weak transcription	Gastric	stomach
6	chr2:54733800-54742200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:54734600-54740800	Enhancers	Placenta Amnion	Placenta Amnion
8	chr2:54735600-54740800	Enhancers	Brain Angular Gyrus	brain
9	chr2:54735800-54740600	Enhancers	Brain Hippocampus Middle	brain
10	chr2:54735800-54741000	Enhancers	Brain Substantia Nigra	brain
11	chr2:54736600-54740800	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr2:54737000-54751400	Weak transcription	HUVEC	blood vessel
13	chr2:54737600-54743200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:54737600-54753800	Weak transcription	Fetal Brain Male	brain
15	chr2:54738200-54743200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:54738200-54743800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:54738200-54746200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:54738200-54746400	Weak transcription	NHLF	lung
19	chr2:54738200-54748200	Weak transcription	Fetal Stomach	stomach
20	chr2:54738200-54751600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:54738400-54743200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:54738400-54743400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:54738400-54746200	Weak transcription	A549	lung
24	chr2:54738400-54751400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:54739000-54740600	Enhancers	Liver	Liver
26	chr2:54739000-54740600	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr2:54739000-54740800	Enhancers	Brain Anterior Caudate	brain
28	chr2:54739000-54741000	Enhancers	Adipose Nuclei	Adipose
29	chr2:54739000-54741000	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr2:54739000-54742400	Enhancers	Fetal Lung	lung
31	chr2:54739200-54740800	Enhancers	HSMMtube	muscle
32	chr2:54739200-54741000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:54739200-54742600	Enhancers	Fetal Heart	heart
34	chr2:54739400-54740600	Enhancers	Stomach Smooth Muscle	stomach
35	chr2:54739400-54740600	Enhancers	HepG2	liver
36	chr2:54739400-54746400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:54739800-54740600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:54739800-54740600	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr2:54739800-54740600	Enhancers	Right Ventricle	heart
40	chr2:54739800-54740800	Enhancers	Colon Smooth Muscle	Colon
41	chr2:54739800-54740800	Enhancers	Fetal Thymus	thymus
42	chr2:54739800-54740800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr2:54739800-54740800	Enhancers	Dnd41	blood
44	chr2:54740000-54740600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:54740000-54740600	Enhancers	NHDF-Ad	bronchial
46	chr2:54740000-54740600	Enhancers	Osteobl	bone
47	chr2:54740000-54740800	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr2:54740000-54740800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:54740000-54740800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:54740000-54740800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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