Variant report

Variant	rs13190457
Chromosome Location	chr5:127762931-127762932
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	chr5:127759519..127761302-chr5:127762913..127765694,2	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]
rs11738659	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11741832	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11742635	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13179424	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13180243	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13182859	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17677069	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs331068	0.86[ASN][1000 genomes]
rs34806389	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35776217	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3805651	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805653	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828661	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62391604	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv531991	chr5:127624564-127966085	Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv599698	chr5:127744825-127850855	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
3	nsv1015650	chr5:127745955-127866566	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
4	esv2763497	chr5:127745955-127882468	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127725800-127765600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:127739200-127789000	Weak transcription	Left Ventricle	heart
3	chr5:127743400-127771800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:127745200-127773800	Weak transcription	Right Ventricle	heart
5	chr5:127746000-127777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:127747400-127772400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:127747600-127784400	Weak transcription	Placenta	Placenta
8	chr5:127748800-127772400	Weak transcription	NH-A	brain
9	chr5:127749800-127763400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:127749800-127772400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:127751200-127772400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:127752200-127764000	Weak transcription	Fetal Stomach	stomach
13	chr5:127754400-127772200	Weak transcription	NHEK	skin
14	chr5:127756800-127772400	Weak transcription	HMEC	breast
15	chr5:127758400-127781800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr5:127759800-127778800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:127760000-127763000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:127760000-127771800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:127760000-127772400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:127760200-127767000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr5:127760200-127772800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:127760600-127764000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:127760600-127764400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:127760600-127764600	Enhancers	Fetal Heart	heart
25	chr5:127760600-127783200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:127760600-127791400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:127762000-127763200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:127762200-127763200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr5:127762400-127769200	Weak transcription	Fetal Kidney	kidney
30	chr5:127762800-127764600	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links