Variant report

Variant	rs9873329
Chromosome Location	chr3:23467026-23467027
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	chr3:23466052..23468838-chr3:23474911..23476655,2	MCF-7	breast:

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1007332	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs1011754	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10510537	0.88[JPT][hapmap]
rs13059557	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13063183	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13063986	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13066741	0.84[TSI][hapmap]
rs13070865	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13076527	0.84[TSI][hapmap]
rs13077333	0.80[AMR][1000 genomes]
rs13083654	0.92[CEU][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes]
rs13084327	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13087234	0.92[CEU][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes]
rs13089963	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13090303	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13095736	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13095887	0.84[JPT][hapmap]
rs13095960	0.80[EUR][1000 genomes]
rs13098494	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1463835	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17012844	0.88[JPT][hapmap]
rs17012852	0.88[JPT][hapmap]
rs17012861	0.88[JPT][hapmap]
rs17012897	0.80[AMR][1000 genomes]
rs17012943	0.88[JPT][hapmap]
rs17012959	0.88[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap]
rs17012969	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs17012988	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs17012998	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs17013003	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs17013023	0.81[ASN][1000 genomes]
rs17013026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17013029	1.00[JPT][hapmap]
rs17013035	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17013049	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs17013104	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17013116	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17013125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17013128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17013152	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17013216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17013219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17013223	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17013241	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17013245	1.00[CHB][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs17013286	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17013314	0.98[ASN][1000 genomes]
rs17013320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17013322	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17013333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17013344	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17013348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17013383	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17013390	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs17013393	0.92[ASN][1000 genomes]
rs17013398	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs17013406	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs17013409	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs17013418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17013422	0.86[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs17013429	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17013433	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs17345745	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17404982	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1985664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs34011881	0.98[ASN][1000 genomes]
rs34108997	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34239585	0.80[AMR][1000 genomes]
rs34646795	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34896901	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34928302	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34972244	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35024744	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35038414	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35059447	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35098118	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35236373	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35320722	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35743404	0.80[AMR][1000 genomes]
rs35966355	0.81[ASN][1000 genomes]
rs35982877	0.87[ASN][1000 genomes]
rs36123653	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4574222	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs57427415	0.98[ASN][1000 genomes]
rs58336807	0.81[ASN][1000 genomes]
rs59034251	0.89[ASN][1000 genomes]
rs60410861	0.81[ASN][1000 genomes]
rs61707213	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71322175	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71322180	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71322181	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71322182	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71322186	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71322188	0.94[EUR][1000 genomes]
rs983288	0.95[ASN][1000 genomes]
rs9857217	0.92[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv876624	chr3:23385877-23483536	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv876625	chr3:23390301-23509597	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1012236	chr3:23408427-23469063	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1010032	chr3:23408985-23469063	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9873329	UBE2E2	cis	cerebellum	SCAN
rs9873329	THRB	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23447000-23479600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:23464200-23471400	Weak transcription	Psoas Muscle	Psoas
3	chr3:23465200-23467200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr3:23465600-23467200	Weak transcription	Fetal Heart	heart
5	chr3:23465800-23467400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr3:23466000-23467400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:23466600-23467400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:23466600-23467400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr3:23466600-23467400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr3:23466600-23467400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr3:23467000-23467400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:23467000-23471800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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