Variant report

Variant	rs976741
Chromosome Location	chr5:80561258-80561259
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80559870..80562227-chr5:80563019..80565306,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10036376	1.00[JPT][hapmap]
rs10514215	1.00[JPT][hapmap]
rs12652649	0.85[TSI][hapmap]
rs13159978	0.88[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes]
rs13160378	0.83[ASN][1000 genomes]
rs13184427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13187211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16878563	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16878572	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17294956	1.00[JPT][hapmap]
rs2270825	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291940	0.90[GIH][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs2406555	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34198027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34378267	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34755999	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35244045	0.83[ASN][1000 genomes]
rs35646117	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35813740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35864788	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6859306	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6872504	0.88[AMR][1000 genomes]
rs6899067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750728	1.00[JPT][hapmap]
rs7725743	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598750	chr5:80503528-80599578	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80528000-80564400	Weak transcription	Hela-S3	cervix
2	chr5:80531200-80564200	Weak transcription	HepG2	liver
3	chr5:80541800-80564400	Weak transcription	A549	lung
4	chr5:80543800-80565600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:80544000-80564200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:80544000-80564400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:80544200-80561400	Weak transcription	NHLF	lung
8	chr5:80544200-80564600	Weak transcription	HSMMtube	muscle
9	chr5:80545400-80565200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr5:80545800-80564800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:80546600-80564600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:80548800-80568000	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr5:80549200-80561400	Weak transcription	Liver	Liver
14	chr5:80549200-80562000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:80549400-80565800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:80549400-80565800	Weak transcription	Lung	lung
17	chr5:80550400-80563800	Weak transcription	NHEK	skin
18	chr5:80550400-80564200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:80550800-80564000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr5:80551200-80562200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:80551200-80562600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:80551200-80564200	Weak transcription	Fetal Intestine Large	intestine
23	chr5:80551200-80564800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr5:80551200-80565000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:80551400-80564400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:80552800-80567200	Weak transcription	Brain Anterior Caudate	brain
27	chr5:80553000-80564800	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:80554400-80563600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr5:80554600-80563800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:80554600-80576400	Weak transcription	Pancreas	Pancrea
31	chr5:80555200-80564600	Weak transcription	Brain Hippocampus Middle	brain
32	chr5:80555200-80564800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr5:80555200-80568600	Weak transcription	Fetal Stomach	stomach
34	chr5:80555600-80562600	Weak transcription	Right Ventricle	heart
35	chr5:80555600-80564000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr5:80555600-80564800	Weak transcription	Gastric	stomach
37	chr5:80555600-80565600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr5:80555800-80561600	Weak transcription	Brain Substantia Nigra	brain
39	chr5:80555800-80564200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr5:80555800-80564800	Weak transcription	Aorta	Aorta
41	chr5:80556000-80565800	Weak transcription	Adipose Nuclei	Adipose
42	chr5:80558000-80564400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr5:80558200-80568000	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr5:80558800-80564000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr5:80558800-80565800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr5:80559200-80563800	Strong transcription	Left Ventricle	heart
47	chr5:80559600-80568400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr5:80559800-80567200	Weak transcription	Fetal Muscle Leg	muscle
49	chr5:80560000-80561800	Weak transcription	Fetal Heart	heart
50	chr5:80560000-80566000	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links