Variant report

Variant	rs1024758
Chromosome Location	chr4:15427498-15427499
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr4:15427189-15427505	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr4:15427126-15427515	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr4:15427161-15427534	MCF10A-Er-Src	breast:	n/a	chr4:15427248-15427256
4	FOS	chr4:15427125-15427554	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr4:15427102-15427545	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr4:15427201-15427528	MCF10A-Er-Src	breast:	n/a	chr4:15427248-15427256

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15401621..15404342-chr4:15426041..15427712,2	MCF-7	breast:

Variant related genes	Relation type
C1QTNF7	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10003338	0.80[EUR][1000 genomes]
rs1024759	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461112	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1048037	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs10488970	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12233742	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13104095	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13106702	0.80[EUR][1000 genomes]
rs13114788	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13116208	0.86[CHD][hapmap]
rs13120744	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13123050	0.92[ASN][1000 genomes]
rs13123785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13124984	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13129124	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13132007	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13132446	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13132604	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13138481	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13138554	0.90[ASN][1000 genomes]
rs16891929	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16891934	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16891939	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17469724	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1990524	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2160046	0.80[EUR][1000 genomes]
rs2192355	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2192356	0.84[CHD][hapmap]
rs28561808	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34028526	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34351987	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34352292	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34400909	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34496443	0.92[ASN][1000 genomes]
rs35301498	0.92[ASN][1000 genomes]
rs35465107	0.90[ASN][1000 genomes]
rs35539860	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35866305	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35971217	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3797006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58479200	0.92[ASN][1000 genomes]
rs59684117	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61240629	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62289285	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66696244	0.91[ASN][1000 genomes]
rs67391897	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68012715	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71601473	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71601477	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs722235	0.90[ASN][1000 genomes]
rs7442554	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1024758	HS3ST1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15416800-15429000	Weak transcription	Fetal Lung	lung
2	chr4:15419000-15428600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:15419800-15428600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr4:15420800-15428800	Weak transcription	Fetal Stomach	stomach
5	chr4:15423000-15428400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:15423200-15428400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:15423200-15428600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr4:15423200-15429000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr4:15423200-15429000	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:15425200-15428000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:15425200-15428000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:15425200-15428000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:15425400-15428800	Enhancers	NHEK	skin
14	chr4:15426000-15428000	Enhancers	HMEC	breast
15	chr4:15426200-15428400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:15427000-15431400	Active TSS	Aorta	Aorta
17	chr4:15427200-15428000	Enhancers	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links