Variant report

Variant	rs4689063
Chromosome Location	chr4:7048419-7048420
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	RUNX3	chr4:7048373-7048789	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:7048401-7048557	K562	blood:	n/a	n/a
3	RUNX3	chr4:7048350-7048720	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:6912685..6914453-chr4:7047994..7050583,2	MCF-7	breast:
2	chr4:7041999..7051916-chr4:7066728..7075643,37	MCF-7	breast:
3	chr4:7047952..7049903-chr4:7053524..7056109,2	MCF-7	breast:
4	chr4:7042421..7051559-chr4:7062214..7072674,24	MCF-7	breast:

Variant related genes	Relation type
CCDC96	TF binding region
ENSG00000245748	TF binding region
ENSG00000109519	Chromatin interaction
ENSG00000173011	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10012093	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10937781	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13113578	0.95[EUR][1000 genomes]
rs3951347	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4513569	0.95[EUR][1000 genomes]
rs4689062	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4689582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4689588	0.95[EUR][1000 genomes]
rs62291193	0.81[EUR][1000 genomes]
rs62291194	0.81[EUR][1000 genomes]
rs62291195	0.81[EUR][1000 genomes]
rs62291196	0.81[EUR][1000 genomes]
rs6814746	0.95[EUR][1000 genomes]
rs6832413	0.95[EUR][1000 genomes]
rs6841824	0.95[EUR][1000 genomes]
rs6849547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7666504	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7699619	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs871133	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs907522	0.95[EUR][1000 genomes]
rs907524	0.95[EUR][1000 genomes]
rs907525	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9985704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
11	esv1801315	chr4:7044007-7052777	Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	esv1835149	chr4:7044007-7052777	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv593556	chr4:7044447-7048842	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	esv1798014	chr4:7044504-7052182	Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7045800-7049400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr4:7046200-7048800	Flanking Active TSS	HSMM	muscle
3	chr4:7046200-7068600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:7046400-7049000	Flanking Active TSS	GM12878-XiMat	blood
5	chr4:7046400-7049800	Enhancers	Primary B cells from peripheral blood	blood
6	chr4:7046400-7049800	Genic enhancers	Spleen	Spleen
7	chr4:7046600-7048600	Enhancers	Small Intestine	intestine
8	chr4:7046600-7049400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:7046600-7050400	Enhancers	Lung	lung
10	chr4:7046600-7050800	Genic enhancers	Fetal Muscle Leg	muscle
11	chr4:7046600-7051400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr4:7046600-7053800	Weak transcription	A549	lung
13	chr4:7046600-7055600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr4:7046600-7055600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr4:7046600-7055800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr4:7046600-7062600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:7046800-7048800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:7046800-7048800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr4:7046800-7048800	Genic enhancers	Fetal Stomach	stomach
20	chr4:7046800-7049000	Enhancers	Fetal Thymus	thymus
21	chr4:7046800-7049200	Enhancers	HSMMtube	muscle
22	chr4:7046800-7049400	Enhancers	Liver	Liver
23	chr4:7046800-7049400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
24	chr4:7046800-7049800	Enhancers	Left Ventricle	heart
25	chr4:7046800-7050000	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr4:7046800-7050000	Genic enhancers	Fetal Muscle Trunk	muscle
27	chr4:7046800-7050000	Enhancers	Psoas Muscle	Psoas
28	chr4:7046800-7062000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:7047000-7048600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:7047000-7048600	Enhancers	Fetal Brain Male	brain
31	chr4:7047000-7048600	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr4:7047000-7048800	Enhancers	NHDF-Ad	bronchial
33	chr4:7047000-7049400	Enhancers	Colonic Mucosa	Colon
34	chr4:7047000-7049400	Enhancers	Ovary	ovary
35	chr4:7047000-7049400	Enhancers	Right Ventricle	heart
36	chr4:7047000-7049600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:7047000-7049800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr4:7047000-7049800	Enhancers	Right Atrium	heart
39	chr4:7047000-7050000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr4:7047000-7053000	Weak transcription	NHLF	lung
41	chr4:7047000-7056000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr4:7047000-7056200	Weak transcription	HUVEC	blood vessel
43	chr4:7047000-7057400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr4:7047000-7059600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:7047000-7061200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr4:7047200-7048600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:7047200-7049400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
48	chr4:7047200-7049400	Genic enhancers	Primary T cells from cord blood	blood
49	chr4:7047200-7049400	Enhancers	Fetal Heart	heart
50	chr4:7047200-7049800	Enhancers	Primary T helper cells fromperipheralblood	blood

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