Variant report

Variant	rs56939666
Chromosome Location	chr1:47084231-47084232
allele	A/C/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	MAFF	chr1:47084104-47084252	HepG2	liver:	n/a	n/a
2	ARID3A	chr1:47083799-47084297	HepG2	liver:	n/a	n/a
3	MAFK	chr1:47084022-47084245	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47068429..47072503-chr1:47081068..47085092,4	MCF-7	breast:

Variant related genes	Relation type
MOB3C	TF binding region
MKNK1	TF binding region
ENSG00000079277	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs28364800	0.81[AMR][1000 genomes]
rs3753358	0.81[AMR][1000 genomes]
rs61565631	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6666069	0.85[ASN][1000 genomes]
rs6703563	0.92[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	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv870392	chr1:47040676-47095097	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv522319	chr1:47080741-47094267	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47082800-47089600	Weak transcription	Small Intestine	intestine
2	chr1:47083000-47085600	Enhancers	GM12878-XiMat	blood
3	chr1:47083000-47085800	Enhancers	Primary B cells from peripheral blood	blood
4	chr1:47083000-47088000	Weak transcription	Spleen	Spleen
5	chr1:47083000-47090800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:47083000-47094400	Weak transcription	Primary T cells from cord blood	blood
7	chr1:47083000-47094600	Weak transcription	Right Ventricle	heart
8	chr1:47083000-47097200	Weak transcription	Gastric	stomach
9	chr1:47083000-47100000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:47083200-47084400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:47083200-47084400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr1:47083200-47084800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:47083200-47087000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:47083200-47087000	Weak transcription	HSMM	muscle
15	chr1:47083200-47087400	Weak transcription	Fetal Intestine Large	intestine
16	chr1:47083200-47087400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:47083200-47087600	Weak transcription	NHEK	skin
18	chr1:47083200-47088000	Weak transcription	Placenta	Placenta
19	chr1:47083200-47088000	Weak transcription	NH-A	brain
20	chr1:47083200-47094400	Weak transcription	Brain Angular Gyrus	brain
21	chr1:47083200-47094600	Weak transcription	Liver	Liver
22	chr1:47083200-47095400	Weak transcription	Fetal Thymus	thymus
23	chr1:47083200-47095600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:47083200-47097200	Weak transcription	Primary B cells from cord blood	blood
25	chr1:47083200-47097200	Weak transcription	Aorta	Aorta
26	chr1:47083200-47097200	Weak transcription	Thymus	Thymus
27	chr1:47083200-47100200	Weak transcription	Psoas Muscle	Psoas
28	chr1:47083200-47104600	Weak transcription	Stomach Mucosa	stomach
29	chr1:47083200-47115000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr1:47083400-47084400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:47083400-47086600	Weak transcription	Hela-S3	cervix
32	chr1:47083400-47086600	Enhancers	K562	blood
33	chr1:47083400-47087400	Weak transcription	Colonic Mucosa	Colon
34	chr1:47083400-47087400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:47083400-47087600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:47083400-47087600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:47083400-47087800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:47083400-47087800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:47083400-47089200	Weak transcription	Right Atrium	heart
40	chr1:47083400-47092200	Weak transcription	Pancreas	Pancrea
41	chr1:47083400-47094200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:47083400-47094200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:47083400-47094600	Weak transcription	Adipose Nuclei	Adipose
44	chr1:47083400-47094800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr1:47083400-47095000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:47083400-47095600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:47083400-47095600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:47083400-47095600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:47083400-47095600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:47083400-47096800	Weak transcription	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links