Variant report

Variant	rs542444
Chromosome Location	chr6:44800015-44800016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 124 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs1023091	0.94[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1028944	0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs10484627	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs10948185	0.89[CHD][hapmap]
rs10948187	0.86[CHD][hapmap]
rs10948188	0.86[CHD][hapmap]
rs10948190	0.86[CHD][hapmap]
rs10948194	0.86[CHD][hapmap]
rs10948197	0.86[CHD][hapmap]
rs1159131	0.83[CHD][hapmap]
rs12196818	0.84[CHD][hapmap]
rs12214778	0.86[CHD][hapmap]
rs12525773	0.87[ASN][1000 genomes]
rs12526711	0.83[JPT][hapmap]
rs12526755	0.87[ASN][1000 genomes]
rs12527908	0.91[ASN][1000 genomes]
rs12528232	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs12529522	0.88[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs12530016	0.88[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs12661902	0.86[ASN][1000 genomes]
rs12663530	0.88[ASN][1000 genomes]
rs12663798	0.87[ASN][1000 genomes]
rs13199289	0.82[ASN][1000 genomes]
rs13202672	0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13206526	1.00[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13209827	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs13216116	0.86[CHD][hapmap]
rs13216967	0.85[ASN][1000 genomes]
rs1329710	0.86[CHD][hapmap]
rs1329715	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs1329716	0.89[CHD][hapmap]
rs1360195	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs1402599	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1418435	0.86[ASN][1000 genomes]
rs16869119	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16872574	0.98[ASN][1000 genomes]
rs17422760	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs1935549	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1980265	0.86[CHD][hapmap]
rs2139863	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs227840	0.81[AMR][1000 genomes]
rs227852	1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[MEX][hapmap]
rs227853	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[MEX][hapmap]
rs227857	0.84[ASN][1000 genomes]
rs2396369	0.86[CHD][hapmap]
rs2396372	0.89[CHD][hapmap]
rs2894599	0.98[ASN][1000 genomes]
rs34243039	0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34286542	0.86[ASN][1000 genomes]
rs34776198	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34817919	0.98[ASN][1000 genomes]
rs35103634	0.87[ASN][1000 genomes]
rs35687006	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs35704584	0.87[ASN][1000 genomes]
rs35856781	0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35908738	0.87[ASN][1000 genomes]
rs36105034	0.86[ASN][1000 genomes]
rs3778507	0.86[CHD][hapmap]
rs3799965	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3799966	0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3799967	0.88[JPT][hapmap]
rs3799969	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3799970	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3799971	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs3799972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3799973	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs3799974	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3799976	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs3799977	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs3799979	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs3799984	0.83[JPT][hapmap]
rs3799986	0.86[CHD][hapmap]
rs3799987	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs3823252	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3997503	0.86[ASN][1000 genomes]
rs4475320	0.87[ASN][1000 genomes]
rs4512220	0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs4711809	0.88[CHB][hapmap];0.89[CHD][hapmap];0.84[ASN][1000 genomes]
rs4714812	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs4714825	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4714827	0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4714828	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs4714829	0.87[ASN][1000 genomes]
rs4714830	0.86[CHD][hapmap]
rs4714834	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs494982	0.86[CHD][hapmap]
rs524492	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs562016	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs59945128	0.87[ASN][1000 genomes]
rs608941	0.86[CHD][hapmap]
rs609643	0.84[ASN][1000 genomes]
rs609699	0.84[ASN][1000 genomes]
rs636845	0.86[CHD][hapmap]
rs66642874	0.98[ASN][1000 genomes]
rs67597621	0.97[ASN][1000 genomes]
rs67911131	0.89[ASN][1000 genomes]
rs6904015	0.88[JPT][hapmap]
rs6904584	0.91[ASN][1000 genomes]
rs6910294	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs6919161	0.94[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs720988	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs720989	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72664272	0.96[ASN][1000 genomes]
rs72664273	0.97[ASN][1000 genomes]
rs72664274	0.98[ASN][1000 genomes]
rs7746032	0.86[ASN][1000 genomes]
rs7754378	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs7754698	0.86[JPT][hapmap]
rs7769218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9296450	0.89[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs9367211	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs9369514	0.83[JPT][hapmap]
rs9369516	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs9395051	0.86[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs9463017	0.86[ASN][1000 genomes]
rs9463039	0.96[ASN][1000 genomes]
rs9463040	0.96[ASN][1000 genomes]
rs9472331	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9472335	0.86[ASN][1000 genomes]
rs9472376	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9472407	0.82[JPT][hapmap]
rs9472409	0.86[CHD][hapmap]
rs9472414	0.89[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs9885796	0.86[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs542444	SUPT3H	cis	multi-tissue	Pritchard
rs542444	PRPH2	cis	cerebellum	SCAN
rs542444	SUPT3H	cis	lymphoblastoid	seeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44791000-44805600	Weak transcription	Ovary	ovary
2	chr6:44792000-44811600	Weak transcription	Pancreas	Pancrea
3	chr6:44796800-44800200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr6:44796800-44800200	Enhancers	HSMMtube	muscle
5	chr6:44796800-44800400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:44797000-44800600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr6:44797400-44800200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:44798200-44800800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:44798200-44811200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:44798400-44800800	Weak transcription	GM12878-XiMat	blood
11	chr6:44798400-44822800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:44798600-44810600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr6:44798800-44801200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr6:44799000-44800200	Enhancers	H9 Cell Line	embryonic stem cell
15	chr6:44799000-44800400	Enhancers	H1 Cell Line	embryonic stem cell
16	chr6:44799000-44800400	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr6:44799000-44800400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr6:44799000-44802600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:44799200-44800400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:44799200-44802000	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr6:44799200-44806000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:44799400-44801000	Weak transcription	Adipose Nuclei	Adipose
23	chr6:44799600-44801800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:44799800-44800400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr6:44799800-44803000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:44800000-44804800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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