Variant report

Variant	rs2731840
Chromosome Location	chr5:106761136-106761137
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	chr3:105500783..105501463-chr5:106760926..106761803,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs252803	0.84[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs252804	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs252805	0.83[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs252808	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs252811	0.89[CEU][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.83[EUR][1000 genomes]
rs252812	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs252818	0.89[CEU][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes]
rs252819	0.89[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs252983	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs252984	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2562525	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2731839	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs431982	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs467472	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs468998	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106738800-106761600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:106739600-106762600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:106751600-106764400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr5:106751800-106765800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:106751800-106767800	Weak transcription	Stomach Mucosa	stomach
6	chr5:106752000-106761600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr5:106752600-106761600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:106753400-106764400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:106754000-106767600	Weak transcription	Fetal Stomach	stomach
10	chr5:106754200-106763800	Weak transcription	GM12878-XiMat	blood
11	chr5:106754400-106761200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:106754800-106762200	Weak transcription	Fetal Lung	lung
13	chr5:106756400-106768200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:106756600-106772000	Weak transcription	Esophagus	oesophagus
15	chr5:106758200-106761600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:106758200-106761600	Enhancers	Hela-S3	cervix
17	chr5:106758200-106762400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:106758600-106761600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:106758600-106761600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:106758600-106761800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:106758600-106763800	Weak transcription	Fetal Heart	heart
22	chr5:106758600-106765800	Weak transcription	Aorta	Aorta
23	chr5:106758600-106765800	Weak transcription	Fetal Kidney	kidney
24	chr5:106758600-106767800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:106758600-106767800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr5:106758600-106767800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr5:106758600-106767800	Weak transcription	Left Ventricle	heart
28	chr5:106758600-106771200	Weak transcription	Right Ventricle	heart
29	chr5:106758600-106772000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:106758600-106785000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr5:106759000-106761400	Enhancers	HMEC	breast
32	chr5:106759000-106762600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr5:106759000-106762600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:106759200-106761200	Enhancers	NHEK	skin
35	chr5:106759200-106762800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:106759400-106761200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:106759400-106761600	Enhancers	NHDF-Ad	bronchial
38	chr5:106759400-106762200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:106759400-106762200	Enhancers	NH-A	brain
40	chr5:106759400-106762400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:106759400-106762400	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr5:106759400-106762400	Enhancers	Osteobl	bone
43	chr5:106759400-106764200	Enhancers	HSMM	muscle
44	chr5:106759600-106762200	Enhancers	Placenta Amnion	Placenta Amnion
45	chr5:106759600-106767600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr5:106760200-106762200	Flanking Active TSS	A549	lung
47	chr5:106760200-106762200	Enhancers	HSMMtube	muscle
48	chr5:106760200-106762400	Enhancers	NHLF	lung
49	chr5:106760400-106762200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:106760400-106763200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links