Variant report

Variant	rs4689583
Chromosome Location	chr4:7054399-7054400
allele	A/G
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	POLR2A	chr4:7053710-7056312	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:7052540..7054549-chr4:7068583..7070696,2	MCF-7	breast:
2	chr4:7047952..7049903-chr4:7053524..7056109,2	MCF-7	breast:
3	chr4:6987851..6990703-chr4:7053695..7056080,2	MCF-7	breast:
4	chr4:7052919..7061052-chr4:7065851..7072132,10	MCF-7	breast:

Variant related genes	Relation type
TADA2B	TF binding region
ENSG00000132405	Chromatin interaction
ENSG00000109519	Chromatin interaction
ENSG00000245748	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs41365350	1.00[GIH][hapmap]
rs41394850	1.00[GIH][hapmap]
rs41499144	1.00[GIH][hapmap]
rs4513569	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs4689574	1.00[CEU][hapmap]
rs4689584	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4689589	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6819148	1.00[GIH][hapmap]
rs907522	0.83[AMR][1000 genomes]
rs9985704	1.00[MEX][hapmap]

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	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757919	chr4:6988148-7269901	Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv2759221	chr4:6988148-7269901	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv428436	chr4:6988148-7269901	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv469847	chr4:7003525-7168441	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv878531	chr4:7006541-7129556	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv878532	chr4:7010504-7055603	Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv878533	chr4:7032180-7063524	Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv4217	chr4:7035512-7080230	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4689583	GNB1L	trans	brain	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7046200-7068600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:7046600-7055600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr4:7046600-7055600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr4:7046600-7055800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:7046600-7062600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:7046800-7062000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:7047000-7056000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:7047000-7056200	Weak transcription	HUVEC	blood vessel
9	chr4:7047000-7057400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:7047000-7059600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:7047000-7061200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr4:7047200-7055600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:7047200-7056200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr4:7047200-7059600	Weak transcription	NH-A	brain
15	chr4:7047400-7059200	Strong transcription	Fetal Intestine Small	intestine
16	chr4:7047400-7062400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:7047600-7056400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:7047800-7055600	Genic enhancers	Primary T cells fromperipheralblood	blood
19	chr4:7047800-7056000	Weak transcription	Osteobl	bone
20	chr4:7047800-7062200	Weak transcription	Hela-S3	cervix
21	chr4:7048000-7054400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr4:7048000-7057000	Weak transcription	HMEC	breast
23	chr4:7048000-7062800	Weak transcription	Fetal Kidney	kidney
24	chr4:7048400-7055800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:7048600-7055000	Weak transcription	Fetal Lung	lung
26	chr4:7048600-7055800	Weak transcription	Aorta	Aorta
27	chr4:7048600-7061400	Weak transcription	Small Intestine	intestine
28	chr4:7048600-7062600	Weak transcription	Fetal Brain Male	brain
29	chr4:7048800-7054600	Strong transcription	Fetal Stomach	stomach
30	chr4:7048800-7055400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:7048800-7055800	Weak transcription	HepG2	liver
32	chr4:7048800-7056000	Weak transcription	NHDF-Ad	bronchial
33	chr4:7049000-7054600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr4:7049000-7055400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr4:7049000-7060400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr4:7049200-7054400	Weak transcription	HSMMtube	muscle
37	chr4:7049400-7055200	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr4:7049400-7061400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr4:7049600-7055400	Weak transcription	GM12878-XiMat	blood
40	chr4:7049800-7055400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
41	chr4:7049800-7060600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:7049800-7066800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:7050000-7056400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:7050200-7058600	Strong transcription	Fetal Intestine Large	intestine
45	chr4:7050400-7055000	Enhancers	Fetal Heart	heart
46	chr4:7050400-7055600	Enhancers	Left Ventricle	heart
47	chr4:7050400-7056200	Genic enhancers	Lung	lung
48	chr4:7050600-7054800	Enhancers	Liver	Liver
49	chr4:7051000-7055800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr4:7051200-7054400	Genic enhancers	Brain Inferior Temporal Lobe	brain

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