Variant report

Variant	rs9463039
Chromosome Location	chr6:44752124-44752125
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	chr6:44749501..44752390-chr6:44755205..44757240,2	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12192367	0.84[JPT][hapmap]
rs12525773	0.83[ASN][1000 genomes]
rs12526755	0.84[ASN][1000 genomes]
rs12527908	0.87[ASN][1000 genomes]
rs12529522	0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs12530016	0.88[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs12661902	0.82[ASN][1000 genomes]
rs12663530	0.85[ASN][1000 genomes]
rs12663798	0.84[ASN][1000 genomes]
rs13202672	0.96[ASN][1000 genomes]
rs13206526	0.94[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs13216967	0.82[ASN][1000 genomes]
rs1329715	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs1360195	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs1402599	0.94[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs1418435	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16869119	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs16872574	0.95[ASN][1000 genomes]
rs1935549	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2038555	0.81[ASN][1000 genomes]
rs2139863	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs227830	0.81[AMR][1000 genomes]
rs227832	0.81[AMR][1000 genomes]
rs227833	0.83[AMR][1000 genomes]
rs227835	0.85[AMR][1000 genomes]
rs227836	0.81[AMR][1000 genomes]
rs227839	0.86[AMR][1000 genomes]
rs227840	0.85[AMR][1000 genomes]
rs227844	0.86[AMR][1000 genomes]
rs227845	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs227849	0.83[JPT][hapmap]
rs227852	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs227853	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes]
rs227857	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2894599	0.95[ASN][1000 genomes]
rs34243039	0.93[ASN][1000 genomes]
rs34286542	0.83[ASN][1000 genomes]
rs34577161	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34776198	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34817919	0.95[ASN][1000 genomes]
rs35103634	0.84[ASN][1000 genomes]
rs35687006	0.83[ASN][1000 genomes]
rs35704584	0.84[ASN][1000 genomes]
rs35856781	0.93[ASN][1000 genomes]
rs35908738	0.83[ASN][1000 genomes]
rs36105034	0.83[ASN][1000 genomes]
rs3799965	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3799966	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3799969	0.96[ASN][1000 genomes]
rs3799970	0.96[ASN][1000 genomes]
rs3799972	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs3799973	0.81[ASN][1000 genomes]
rs3799974	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs3799987	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs3823252	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs3997503	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4475320	0.84[ASN][1000 genomes]
rs4512220	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs4711797	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4714812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4714821	0.82[ASN][1000 genomes]
rs4714825	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4714827	0.93[ASN][1000 genomes]
rs4714829	0.84[ASN][1000 genomes]
rs524492	0.94[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs542444	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs562016	0.96[ASN][1000 genomes]
rs59945128	0.84[ASN][1000 genomes]
rs609643	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs609699	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs66642874	0.95[ASN][1000 genomes]
rs67597621	0.93[ASN][1000 genomes]
rs67911131	0.86[ASN][1000 genomes]
rs6904584	0.87[ASN][1000 genomes]
rs6910294	0.80[CHB][hapmap]
rs6919161	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs720988	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs720989	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72664272	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72664273	0.94[ASN][1000 genomes]
rs72664274	0.95[ASN][1000 genomes]
rs7746032	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7769218	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9296450	0.82[ASN][1000 genomes]
rs9463017	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9463040	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9472335	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9472376	0.80[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs9472414	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs9885796	0.82[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9463039	SUPT3H	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44751000-44752800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:44751400-44752400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:44752000-44752400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:44752000-44752800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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