Variant report

Variant	rs56290425
Chromosome Location	chr2:46725716-46725717
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46705265..46709008-chr2:46724758..46728950,5	K562	blood:
2	chr2:46724562..46726815-chr2:46734008..46735625,2	MCF-7	breast:
3	chr2:46724349..46729821-chr2:46769212..46772070,6	MCF-7	breast:
4	chr2:46721184..46729524-chr2:46766976..46775977,14	K562	blood:

Variant related genes	Relation type
ENSG00000250565	Chromatin interaction
ENSG00000119729	Chromatin interaction
ENSG00000187600	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs55775849	0.86[AFR][1000 genomes]
rs55939277	0.86[AFR][1000 genomes]
rs56365783	1.00[AFR][1000 genomes]
rs56678855	1.00[AFR][1000 genomes]
rs57596928	0.86[AFR][1000 genomes]
rs59253102	1.00[AFR][1000 genomes]
rs61065239	1.00[AFR][1000 genomes]
rs61169200	1.00[AFR][1000 genomes]
rs73927843	1.00[AFR][1000 genomes]
rs73927846	0.86[AFR][1000 genomes]
rs73927847	1.00[AFR][1000 genomes]
rs73927849	0.86[AFR][1000 genomes]
rs73927866	0.87[AFR][1000 genomes]
rs73927872	0.86[AFR][1000 genomes]
rs73927876	1.00[AFR][1000 genomes]
rs873532	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2756919	chr2:46614235-46756431	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv437435	chr2:46636967-46763587	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv9702	chr2:46668106-46745740	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv817828	chr2:46670146-46739157	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv1000129	chr2:46723102-46733814	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv438326	chr2:46723219-46726210	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46718200-46726600	Weak transcription	Aorta	Aorta
2	chr2:46718400-46726600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:46718600-46726600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr2:46718600-46726600	Weak transcription	Right Ventricle	heart
5	chr2:46718800-46726400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:46718800-46726600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:46718800-46727000	Weak transcription	Spleen	Spleen
8	chr2:46721000-46726600	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:46721200-46726600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:46721200-46726600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:46721200-46726600	Weak transcription	Left Ventricle	heart
12	chr2:46721400-46726600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:46722000-46726600	Weak transcription	Brain Germinal Matrix	brain
14	chr2:46722800-46726600	Weak transcription	Fetal Brain Female	brain
15	chr2:46723200-46726600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:46723200-46726600	Weak transcription	NH-A	brain
17	chr2:46723400-46726600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:46723400-46726600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:46723400-46726600	Weak transcription	NHLF	lung
20	chr2:46723400-46726600	Weak transcription	Osteobl	bone
21	chr2:46724000-46726400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:46724400-46726400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr2:46724600-46726000	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr2:46724600-46726600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr2:46724800-46726600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:46725000-46726600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:46725000-46726600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:46725400-46726400	Enhancers	Hela-S3	cervix
29	chr2:46725400-46726600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:46725600-46726400	Enhancers	Brain Substantia Nigra	brain
31	chr2:46725600-46726600	Weak transcription	Brain Anterior Caudate	brain
32	chr2:46725600-46726600	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links