Variant report

Variant	rs1647386
Chromosome Location	chr15:57094724-57094725
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	chr15:57093337..57095465-chr15:57097017..57099531,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10518872	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11071285	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12437635	1.00[CEU][hapmap];0.88[AMR][1000 genomes]
rs12437714	0.91[AMR][1000 genomes]
rs12437735	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12437753	0.80[AMR][1000 genomes]
rs12438377	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12438572	0.85[AMR][1000 genomes]
rs12438728	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12439116	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12439149	1.00[CEU][hapmap]
rs12439547	1.00[CEU][hapmap]
rs12439563	0.89[EUR][1000 genomes]
rs12439697	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12440006	0.89[EUR][1000 genomes]
rs12440725	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs12440790	1.00[CEU][hapmap]
rs12440891	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs12441200	1.00[CEU][hapmap]
rs12441263	1.00[CEU][hapmap]
rs12441746	0.84[EUR][1000 genomes]
rs12441769	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12441792	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12442069	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12442630	0.91[AMR][1000 genomes]
rs12442642	0.83[AMR][1000 genomes]
rs12442662	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs12442839	0.83[AMR][1000 genomes]
rs12443178	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12903143	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12907983	0.89[EUR][1000 genomes]
rs1364541	0.91[AMR][1000 genomes]
rs1529597	0.87[AMR][1000 genomes]
rs1564557	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs1600829	0.89[EUR][1000 genomes]
rs1600831	0.84[EUR][1000 genomes]
rs1631905	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1647391	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977123	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977170	1.00[CEU][hapmap]
rs17238880	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs17238894	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17238901	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17238950	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17238971	1.00[CEU][hapmap];0.80[AMR][1000 genomes]
rs17819592	0.89[EUR][1000 genomes]
rs17819616	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17819646	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs17819658	0.83[AMR][1000 genomes]
rs17819664	0.83[AMR][1000 genomes]
rs1834199	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2052641	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2161935	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2899599	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3199	0.95[MEX][hapmap]
rs4287503	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4362334	0.87[AMR][1000 genomes]
rs4424865	0.91[AMR][1000 genomes]
rs4774885	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs480701	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6493888	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7176472	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs74015901	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs966807	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv569576	chr15:57012816-57126917	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv833020	chr15:57055947-57216068	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv457162	chr15:57083006-57225766	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv569577	chr15:57083006-57225766	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1647386	SCT	trans	lymphoblastoid	seeQTL
rs1647386	SEPX1	trans	lymphoblastoid	seeQTL
rs1647386	TPM2	trans	lymphoblastoid	seeQTL
rs1647386	CSTA	trans	lymphoblastoid	seeQTL
rs1647386	FOXG1	trans	lymphoblastoid	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57087200-57096200	Weak transcription	HSMM	muscle
2	chr15:57088000-57097800	Weak transcription	Adipose Nuclei	Adipose
3	chr15:57091200-57097200	Weak transcription	Ovary	ovary
4	chr15:57091200-57104200	Weak transcription	Aorta	Aorta
5	chr15:57094200-57095400	Enhancers	Dnd41	blood
6	chr15:57094200-57095600	Enhancers	Fetal Thymus	thymus
7	chr15:57094400-57095200	Enhancers	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links