Variant report

Variant	rs521896
Chromosome Location	chr15:40429772-40429773
allele	C/T
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	RAD21	chr15:40429741-40430145	ECC-1	luminal epithelium:	n/a	n/a
2	RAD21	chr15:40429705-40430200	MCF-7	breast:	n/a	n/a
3	CTCF	chr15:40429746-40430217	HCT-116	colon:	n/a	n/a
4	CTCF	chr15:40429715-40430171	MCF-7	breast:	n/a	n/a
5	CTCF	chr15:40429756-40430136	H1-hESC	embryonic stem cell:	n/a	n/a
6	ZNF384	chr15:40429764-40430116	K562	blood:	n/a	n/a
7	RAD21	chr15:40429696-40430164	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr15:40429733-40429867	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40397083..40397632-chr15:40429201..40430196,2	MCF-7	breast:
2	chr15:40423124..40425673-chr15:40427954..40430256,2	K562	blood:

Variant related genes	Relation type
ENSG00000259239	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10518681	0.98[EUR][1000 genomes]
rs10518682	0.94[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11632939	0.95[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs11634034	0.88[EUR][1000 genomes]
rs11636402	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11637268	0.89[EUR][1000 genomes]
rs11638942	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11854027	0.98[EUR][1000 genomes]
rs11854103	0.98[EUR][1000 genomes]
rs11854965	0.98[EUR][1000 genomes]
rs12438986	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12898627	0.95[EUR][1000 genomes]
rs12899779	0.96[EUR][1000 genomes]
rs12902191	0.98[EUR][1000 genomes]
rs12908093	0.98[EUR][1000 genomes]
rs12910199	0.98[EUR][1000 genomes]
rs12911157	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12913620	0.98[EUR][1000 genomes]
rs12913741	0.98[EUR][1000 genomes]
rs12913803	0.96[EUR][1000 genomes]
rs12915249	0.95[CEU][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12916901	0.98[EUR][1000 genomes]
rs1471583	0.98[EUR][1000 genomes]
rs1565863	0.98[EUR][1000 genomes]
rs1565864	0.98[EUR][1000 genomes]
rs1565865	0.98[EUR][1000 genomes]
rs16970409	0.98[EUR][1000 genomes]
rs1801376	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2277559	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2412480	0.98[EUR][1000 genomes]
rs2412482	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3214012	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34358001	0.93[EUR][1000 genomes]
rs4244573	0.98[EUR][1000 genomes]
rs4244574	0.98[EUR][1000 genomes]
rs4923857	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4924419	0.98[EUR][1000 genomes]
rs4924420	0.98[EUR][1000 genomes]
rs4924424	0.98[EUR][1000 genomes]
rs4924427	0.93[EUR][1000 genomes]
rs4924430	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4924432	0.82[ASN][1000 genomes]
rs492813	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs500693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs597752	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492932	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6492935	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7162894	0.86[EUR][1000 genomes]
rs7164047	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7169518	0.85[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap]
rs7177759	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs797420	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8037190	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs811746	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv3423229	chr15:40417126-40447686	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3500491	chr15:40417175-40446353	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3500492	chr15:40417175-40446353	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40428200-40429800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:40428200-40430200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:40428200-40430200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:40428400-40429800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:40428600-40442200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:40428800-40430200	Enhancers	H1 Cell Line	embryonic stem cell
7	chr15:40429000-40429800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:40429000-40430600	Enhancers	K562	blood
9	chr15:40429400-40429800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:40429400-40429800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:40429600-40429800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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