Variant report

Variant	rs4953759
Chromosome Location	chr2:110400923-110400924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:110370732..110372780-chr2:110400593..110403257,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186522	Chromatin interaction
ENSG00000198142	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs28372574	0.85[AMR][1000 genomes]
rs28699105	0.85[AMR][1000 genomes]
rs2903538	1.00[AMR][1000 genomes]
rs4953757	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4953758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4953839	0.85[AMR][1000 genomes]
rs4953852	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56822430	0.96[AMR][1000 genomes]
rs6751928	0.88[AMR][1000 genomes]
rs72938251	0.85[AMR][1000 genomes]
rs9750479	0.92[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers 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	21 gene(s)	inside rSNPs	diseases
6	nsv1009367	chr2:110349178-110863354	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	esv2762780	chr2:110367969-110462496	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv491837	chr2:110381297-110964737	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv999552	chr2:110396395-110978224	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110393800-110402200	Weak transcription	Fetal Thymus	thymus
2	chr2:110393800-110402600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:110396200-110401800	Weak transcription	Stomach Mucosa	stomach
4	chr2:110396200-110402200	Weak transcription	Lung	lung
5	chr2:110396400-110401200	Weak transcription	Liver	Liver
6	chr2:110396400-110401800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:110396400-110401800	Weak transcription	NHEK	skin
8	chr2:110396400-110401800	Weak transcription	Osteobl	bone
9	chr2:110396600-110402000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:110396600-110402000	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:110396800-110401800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:110396800-110401800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr2:110396800-110401800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:110396800-110401800	Weak transcription	Adipose Nuclei	Adipose
15	chr2:110396800-110401800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:110397000-110401800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:110398200-110401800	Enhancers	HepG2	liver
18	chr2:110400600-110401200	Enhancers	GM12878-XiMat	blood
19	chr2:110400600-110401800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:110400600-110403800	Enhancers	Fetal Intestine Large	intestine
21	chr2:110400600-110406600	Enhancers	Placenta	Placenta
22	chr2:110400800-110401000	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr2:110400800-110401200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:110400800-110403200	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links