Variant report

Variant	rs720989
Chromosome Location	chr6:44765535-44765536
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:44763455..44766382-chr6:44767163..44768857,2	MCF-7	breast:

Extended variants
information (count: 116 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs1023091	0.82[ASN][1000 genomes]
rs10484627	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs10948185	0.89[CHD][hapmap]
rs10948187	0.87[CHD][hapmap]
rs10948188	0.86[CHD][hapmap]
rs10948190	0.87[CHD][hapmap]
rs10948194	0.87[CHD][hapmap]
rs12196818	0.84[CHD][hapmap]
rs12214778	0.87[CHD][hapmap]
rs12525773	0.84[ASN][1000 genomes]
rs12526711	0.83[JPT][hapmap]
rs12526755	0.85[ASN][1000 genomes]
rs12527908	0.88[ASN][1000 genomes]
rs12529522	0.88[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs12530016	0.88[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs12661902	0.83[ASN][1000 genomes]
rs12663530	0.86[ASN][1000 genomes]
rs12663798	0.85[ASN][1000 genomes]
rs13202672	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13206526	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13216116	0.87[CHD][hapmap]
rs13216967	0.83[ASN][1000 genomes]
rs1329715	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs1329716	0.89[CHD][hapmap]
rs1360195	1.00[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs1402599	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1418435	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16869119	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16872574	0.96[ASN][1000 genomes]
rs17338483	1.00[YRI][hapmap]
rs17422760	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs1935549	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1980265	0.87[CHD][hapmap]
rs2139863	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs227852	1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[MEX][hapmap]
rs227853	1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[MEX][hapmap]
rs227857	0.81[ASN][1000 genomes]
rs2396369	0.87[CHD][hapmap]
rs2894599	0.96[ASN][1000 genomes]
rs34243039	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34286542	0.84[ASN][1000 genomes]
rs34577161	0.87[AMR][1000 genomes]
rs34776198	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34817919	0.96[ASN][1000 genomes]
rs35103634	0.85[ASN][1000 genomes]
rs35687006	1.00[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs35704584	0.85[ASN][1000 genomes]
rs35856781	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35908738	0.84[ASN][1000 genomes]
rs36105034	0.84[ASN][1000 genomes]
rs3778507	0.87[CHD][hapmap]
rs3799965	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3799966	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799967	0.88[JPT][hapmap]
rs3799969	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3799970	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3799971	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs3799972	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3799973	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs3799974	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3799976	0.83[JPT][hapmap]
rs3799977	0.87[CHD][hapmap];0.83[JPT][hapmap]
rs3799979	0.87[CHD][hapmap];0.83[JPT][hapmap]
rs3799984	0.83[JPT][hapmap]
rs3799986	0.87[CHD][hapmap]
rs3799987	1.00[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs3823252	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3997503	0.83[ASN][1000 genomes]
rs4475320	0.85[ASN][1000 genomes]
rs4512220	0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs4711797	0.88[AMR][1000 genomes]
rs4714812	1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs4714825	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4714827	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4714828	0.87[CHD][hapmap];0.83[JPT][hapmap]
rs4714829	0.85[ASN][1000 genomes]
rs4714830	0.87[CHD][hapmap]
rs494982	0.86[CHD][hapmap]
rs524492	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs542444	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs562016	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59945128	0.85[ASN][1000 genomes]
rs608941	0.87[CHD][hapmap]
rs609643	0.81[ASN][1000 genomes]
rs609699	0.81[ASN][1000 genomes]
rs636845	0.87[CHD][hapmap]
rs66642874	0.96[ASN][1000 genomes]
rs67597621	0.94[ASN][1000 genomes]
rs67911131	0.86[ASN][1000 genomes]
rs6904015	0.88[JPT][hapmap]
rs6904584	0.88[ASN][1000 genomes]
rs6910294	0.83[JPT][hapmap]
rs6919161	0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs720988	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72664272	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72664273	0.95[ASN][1000 genomes]
rs72664274	0.96[ASN][1000 genomes]
rs7746032	0.83[ASN][1000 genomes]
rs7754378	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs7754698	0.86[JPT][hapmap]
rs7769218	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296450	0.89[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs9367211	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs9369514	0.83[JPT][hapmap]
rs9369516	0.87[CHD][hapmap];0.83[JPT][hapmap]
rs9395051	0.87[CHD][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs9463017	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9463039	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9463040	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9472331	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs9472335	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9472376	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9472407	0.82[JPT][hapmap]
rs9472409	0.87[CHD][hapmap]
rs9472414	0.89[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs9885796	0.83[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs720989	MED20	cis	parietal	SCAN
rs720989	UNC5CL	cis	cerebellum	SCAN
rs720989	SUPT3H	cis	multi-tissue	Pritchard
rs720989	C6orf226	cis	cerebellum	SCAN
rs720989	SUPT3H	cis	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44761800-44776200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:44762000-44768000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:44762400-44765800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:44764200-44766000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr6:44764400-44765600	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr6:44764400-44765800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr6:44765000-44765600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr6:44765000-44766200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:44765000-44767200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr6:44765200-44766000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:44765200-44766600	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr6:44765200-44768800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr6:44765400-44765600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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