Variant report

Variant	rs3922283
Chromosome Location	chr2:40331135-40331136
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	PBX3	chr2:40330349-40331249	SK-N-SH	brain:	n/a	n/a
2	FOS	chr2:40330843-40331203	MCF10A-Er-Src	breast:	n/a	n/a
3	RAD21	chr2:40330248-40331209	IMR90	lung:	n/a	n/a
4	CEBPB	chr2:40330231-40331193	IMR90	lung:	n/a	chr2:40330437-40330448 chr2:40330438-40330447
5	TCF12	chr2:40330393-40331298	SK-N-SH	brain:	n/a	chr2:40331025-40331032
6	PBX3	chr2:40330726-40331246	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr2:40330277-40331353	SK-N-SH	brain:	n/a	chr2:40331025-40331032
8	TEAD4	chr2:40330318-40331180	SK-N-SH	brain:	n/a	n/a
9	FOSL2	chr2:40330258-40331151	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr2:40330293-40331255	SK-N-SH	brain:	n/a	chr2:40331073-40331084 chr2:40331071-40331080

Variant related genes	Relation type
SLC8A1-AS1	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs17025097	0.91[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs4952447	0.92[ASN][1000 genomes]
rs6736628	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916300	chr2:40079899-40339019	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833892	chr2:40188785-40363480	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	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
4	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv873903	chr2:40285145-40382712	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3922283	GABPB2	trans	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40320000-40332200	Enhancers	HSMM	muscle
2	chr2:40320000-40332600	Enhancers	NHDF-Ad	bronchial
3	chr2:40321200-40354600	Weak transcription	Right Ventricle	heart
4	chr2:40322800-40350200	Weak transcription	Fetal Brain Male	brain
5	chr2:40323400-40332600	Enhancers	Osteobl	bone
6	chr2:40326000-40333600	Enhancers	Fetal Heart	heart
7	chr2:40326600-40333400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:40327800-40331200	Enhancers	Fetal Stomach	stomach
9	chr2:40327800-40331400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:40328000-40365600	Weak transcription	Brain Germinal Matrix	brain
11	chr2:40328800-40331600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:40329000-40331200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr2:40329000-40341400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:40329600-40331200	Enhancers	H1 Cell Line	embryonic stem cell
15	chr2:40329600-40331200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr2:40329600-40331200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:40329600-40331200	Enhancers	Fetal Lung	lung
18	chr2:40329600-40331400	Enhancers	Rectal Smooth Muscle	rectum
19	chr2:40329600-40332400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:40329600-40341400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:40329800-40331400	Enhancers	HMEC	breast
22	chr2:40329800-40332600	Weak transcription	Brain Anterior Caudate	brain
23	chr2:40329800-40337400	Weak transcription	Left Ventricle	heart
24	chr2:40329800-40342400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:40329800-40345200	Weak transcription	Fetal Thymus	thymus
26	chr2:40330000-40331200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:40330000-40331400	Enhancers	Colon Smooth Muscle	Colon
28	chr2:40330200-40331200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:40330200-40331400	Enhancers	NHEK	skin
30	chr2:40330200-40331600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:40330400-40332000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr2:40330600-40331400	Enhancers	Ovary	ovary
33	chr2:40330600-40331600	Enhancers	NH-A	brain
34	chr2:40330600-40331800	Enhancers	HSMMtube	muscle
35	chr2:40330600-40332400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr2:40330600-40333400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:40330800-40331400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:40330800-40331600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:40331000-40331200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:40331000-40331200	Enhancers	Aorta	Aorta
41	chr2:40331000-40331200	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr2:40331000-40331200	Enhancers	Placenta Amnion	Placenta Amnion
43	chr2:40331000-40331200	Flanking Active TSS	NHLF	lung
44	chr2:40331000-40331400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:40331000-40332600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:40331000-40332800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:40331000-40340800	Weak transcription	Dnd41	blood

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