Variant report

Variant	rs172649
Chromosome Location	chr16:71596005-71596006
allele	G/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	CBX3	chr16:71595812-71596184	K562	blood:	n/a	n/a
2	GATA3	chr16:71595794-71596082	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000260886	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1035545	0.82[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs1058747	0.83[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap]
rs11075889	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11075890	0.87[ASN][1000 genomes]
rs11075891	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11075892	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11075895	0.82[CHD][hapmap];0.83[GIH][hapmap]
rs11539980	0.83[CEU][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs11643690	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11648240	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11648674	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs11859729	0.82[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap]
rs11862798	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12444484	0.83[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs12447856	0.83[CEU][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs12597065	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs12932850	0.83[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes]
rs1392487	0.83[CEU][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs1477386	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1582589	0.82[CEU][hapmap]
rs16973266	0.82[JPT][hapmap]
rs172650	0.94[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2032920	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2036338	0.83[CEU][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs2113222	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2270830	0.83[CEU][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs2270831	0.83[CEU][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs2270832	0.94[JPT][hapmap]
rs2278031	0.83[CEU][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs2303225	0.86[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes]
rs2334879	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2334883	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2334884	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2432519	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2432520	0.82[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2432524	0.88[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs310331	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs310334	0.81[CHD][hapmap]
rs34764568	0.81[AMR][1000 genomes]
rs35939203	0.84[ASN][1000 genomes]
rs3752681	0.83[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs3813743	0.81[CHD][hapmap]
rs3829537	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4149498	0.81[CHD][hapmap]
rs4444347	0.83[JPT][hapmap]
rs4788544	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788546	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4788547	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4788549	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs4788551	0.83[CEU][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs4788809	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4788812	0.92[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4788814	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4788817	0.92[CEU][hapmap];0.86[CHD][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4788821	0.83[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs4788826	0.82[CEU][hapmap];0.88[JPT][hapmap]
rs4788827	0.83[CEU][hapmap];0.88[JPT][hapmap]
rs62053077	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62053078	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7185997	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs7186717	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7187165	0.81[CHD][hapmap]
rs7187354	0.81[CHD][hapmap]
rs7188406	0.86[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.89[ASN][1000 genomes]
rs7195840	0.83[ASN][1000 genomes]
rs7201754	0.83[GIH][hapmap];0.83[JPT][hapmap]
rs7202288	0.82[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap]
rs7206039	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8044561	0.81[CHD][hapmap]
rs8048057	0.83[CEU][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs8048210	0.83[CEU][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs8058294	0.80[CHB][hapmap]
rs8061970	0.82[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap]
rs8203	0.83[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs918721	0.83[CEU][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs979789	0.88[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap]
rs9921270	0.83[CEU][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs9923264	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9923336	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9925228	0.83[CEU][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs9926110	0.81[CHD][hapmap]
rs9930543	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9932415	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9933680	0.81[CHD][hapmap]
rs9933961	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9936249	0.81[CHD][hapmap]
rs9939455	0.83[CEU][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs9939471	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9939658	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9940142	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9940217	0.82[CEU][hapmap];0.89[JPT][hapmap]

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	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs172649	B3GNT9	cis	parietal	SCAN
rs172649	ZNF23	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71587000-71598000	Weak transcription	Brain Anterior Caudate	brain
2	chr16:71590400-71597600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr16:71593800-71597800	Weak transcription	Fetal Intestine Large	intestine
4	chr16:71596000-71596200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr16:71596000-71597400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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