Variant report

Variant	rs55942328
Chromosome Location	chr4:6990960-6990961
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:6987825-6991466	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:6990131..6992286-chr4:6999504..7002082,2	MCF-7	breast:
2	chr4:6908809..6911215-chr4:6990907..6993739,2	K562	blood:
3	chr4:6782714..6785893-chr4:6989936..6993084,3	K562	blood:
4	chr4:6989642..6991738-chr4:7006793..7008969,2	K562	blood:
5	chr4:6989598..6991738-chr4:7007469..7010160,2	K562	blood:
6	chr4:6783058..6785294-chr4:6987568..6991326,3	MCF-7	breast:
7	chr4:6981814..6984780-chr4:6988944..6991170,2	MCF-7	breast:
8	chr4:6690654..6692400-chr4:6990109..6991782,2	K562	blood:
9	chr4:6909371..6913138-chr4:6987040..6991863,16	MCF-7	breast:
10	chr4:6909040..6912883-chr4:6987028..6993211,15	MCF-7	breast:
11	chr4:6988789..6991540-chr4:7069432..7071324,2	MCF-7	breast:

No data

Variant related genes	Relation type
TBC1D14	TF binding region
ENSG00000246526	Chromatin interaction
ENSG00000132405	Chromatin interaction
ENSG00000109519	Chromatin interaction
ENSG00000170871	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1048009	1.00[EUR][1000 genomes]
rs55633489	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55659111	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55672215	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55833486	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55913461	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56031152	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56074877	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56081162	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56097119	0.87[EUR][1000 genomes]
rs56300156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56320732	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56350643	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56400338	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59742225	0.86[AMR][1000 genomes]
rs59809420	0.82[AMR][1000 genomes]
rs66519732	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66573146	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs66645969	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67067921	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67315413	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67702333	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs68111914	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6836225	0.91[AMR][1000 genomes]
rs6838042	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6838250	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6841389	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6851488	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73088528	0.83[AMR][1000 genomes]
rs73088564	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73202120	1.00[EUR][1000 genomes]
rs73202122	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7668802	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7675281	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7686168	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7686186	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9942188	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][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	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6989600-6991000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:6989600-6991200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:6989600-6991400	Enhancers	Pancreas	Pancrea
4	chr4:6989600-6994400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr4:6989800-6991000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:6989800-6991200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr4:6989800-6991200	Flanking Active TSS	Brain Germinal Matrix	brain
8	chr4:6989800-6991200	Flanking Active TSS	Fetal Brain Female	brain
9	chr4:6989800-6991200	Enhancers	Placenta	Placenta
10	chr4:6989800-6991200	Enhancers	Gastric	stomach
11	chr4:6989800-6991400	Enhancers	Stomach Mucosa	stomach
12	chr4:6989800-6991600	Enhancers	Primary T cells from cord blood	blood
13	chr4:6989800-6991600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr4:6989800-6991600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:6989800-6991600	Enhancers	Liver	Liver
16	chr4:6989800-6991600	Enhancers	Placenta Amnion	Placenta Amnion
17	chr4:6989800-6992000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:6989800-6994000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr4:6989800-6998000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:6990000-6991000	Enhancers	Fetal Stomach	stomach
21	chr4:6990000-6991200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:6990000-6991200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr4:6990000-6991200	Enhancers	Fetal Intestine Large	intestine
24	chr4:6990000-6991400	Enhancers	Lung	lung
25	chr4:6990000-6991600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:6990000-6991800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr4:6990000-6992200	Enhancers	Primary B cells from peripheral blood	blood
28	chr4:6990000-6992600	Enhancers	Spleen	Spleen
29	chr4:6990000-6993000	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr4:6990000-6993200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr4:6990000-6994200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr4:6990000-6997400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr4:6990200-6991000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:6990200-6991000	Enhancers	Fetal Muscle Trunk	muscle
35	chr4:6990200-6991000	Enhancers	Fetal Muscle Leg	muscle
36	chr4:6990200-6991200	Enhancers	Fetal Heart	heart
37	chr4:6990200-6991200	Genic enhancers	Fetal Intestine Small	intestine
38	chr4:6990200-6991200	Enhancers	Fetal Thymus	thymus
39	chr4:6990200-6991400	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr4:6990200-6991400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr4:6990200-6991400	Enhancers	Right Atrium	heart
42	chr4:6990200-6991400	Genic enhancers	Thymus	Thymus
43	chr4:6990200-6991600	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr4:6990200-6991600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:6990200-6991600	Enhancers	Adipose Nuclei	Adipose
46	chr4:6990200-6991600	Enhancers	Fetal Brain Male	brain
47	chr4:6990200-6991800	Enhancers	H1 Cell Line	embryonic stem cell
48	chr4:6990200-6991800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr4:6990200-6991800	Enhancers	Left Ventricle	heart
50	chr4:6990200-6992400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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