Variant report

Variant	rs1322951
Chromosome Location	chr13:53771650-53771651
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	SIN3AK20	chr13:53771395-53772137	MCF-7	breast:	n/a	n/a
2	FOXP2	chr13:53771641-53771854	PFSK-1	brain:	n/a	n/a
3	GATA3	chr13:53771344-53772012	MCF-7	breast:	n/a	chr13:53771717-53771725 chr13:53771996-53772012
4	GATA3	chr13:53771382-53771883	MCF-7	breast:	n/a	chr13:53771717-53771725
5	EBF1	chr13:53771516-53772015	GM12878	blood:	n/a	chr13:53771797-53771808 chr13:53771798-53771807
6	POLR2A	chr13:53771440-53772160	PFSK-1	brain:	n/a	n/a
7	GATA2	chr13:53771548-53772332	SH-SY5Y	brain:	n/a	chr13:53771996-53772012
8	FOXP2	chr13:53771391-53771999	SK-N-MC	brain:	n/a	chr13:53771571-53771583
9	GATA3	chr13:53771547-53771868	T-47D	breast:	n/a	chr13:53771717-53771725
10	EBF1	chr13:53771617-53771934	GM12878	blood:	n/a	chr13:53771797-53771808 chr13:53771798-53771807
11	FOXA1	chr13:53771630-53771889	T-47D	breast:	n/a	chr13:53771727-53771742
12	FOXA1	chr13:53771641-53771975	T-47D	breast:	n/a	chr13:53771727-53771742
13	POLR2A	chr13:53771447-53772020	SK-N-MC	brain:	n/a	n/a
14	GATA3	chr13:53771555-53772155	SH-SY5Y	brain:	n/a	chr13:53771717-53771725 chr13:53771996-53772012
15	KAP1	chr13:53771093-53771916	U2OS	brain:	n/a	n/a
16	GATA3	chr13:53771582-53771859	T-47D	breast:	n/a	chr13:53771717-53771725
17	RAD21	chr13:53771182-53772615	SK-N-SH	brain:	n/a	chr13:53772350-53772369 chr13:53771760-53771773
18	FOXP2	chr13:53771634-53771888	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:53766887..53769388-chr13:53770442..53772910,2	MCF-7	breast:

Variant related genes	Relation type
PCDH8P1	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1016829	0.94[ASN][1000 genomes]
rs1322938	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1322941	0.87[EUR][1000 genomes]
rs1322942	0.88[EUR][1000 genomes]
rs1322943	0.88[EUR][1000 genomes]
rs1322944	0.88[EUR][1000 genomes]
rs1322949	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1322952	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1322955	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322956	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322961	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1322962	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1343602	0.87[EUR][1000 genomes]
rs1407685	0.88[EUR][1000 genomes]
rs1407686	0.81[ASN][1000 genomes]
rs1419218	0.88[EUR][1000 genomes]
rs1853369	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1909648	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1923767	0.88[EUR][1000 genomes]
rs1923768	0.88[EUR][1000 genomes]
rs1923771	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1951722	0.86[EUR][1000 genomes]
rs2015677	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2038649	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2093598	0.88[EUR][1000 genomes]
rs2093599	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2408766	0.88[EUR][1000 genomes]
rs2491124	0.94[ASN][1000 genomes]
rs2759675	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2759706	0.94[ASN][1000 genomes]
rs2759708	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2759709	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2759712	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2759716	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2806936	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2806939	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2806941	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2806956	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2806960	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2806963	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2806964	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2806966	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886202	0.89[EUR][1000 genomes]
rs4886270	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7984963	0.90[ASN][1000 genomes]
rs7994915	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8002513	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs912052	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912054	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs927518	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9527057	1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9536358	0.87[EUR][1000 genomes]
rs9536359	0.89[EUR][1000 genomes]
rs9536363	0.91[EUR][1000 genomes]
rs9536378	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs9568807	0.86[EUR][1000 genomes]
rs9568813	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9568826	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs959222	0.86[EUR][1000 genomes];0.94[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	nsv1050969	chr13:53665927-54064861	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53766400-53774200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:53767400-53771800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr13:53767400-53772000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr13:53770400-53773000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr13:53770400-53773600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr13:53770800-53772200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr13:53770800-53773000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:53770800-53774000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr13:53771200-53773000	Enhancers	Fetal Lung	lung
10	chr13:53771200-53773800	Enhancers	Fetal Brain Female	brain

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