Variant report

Variant	rs16872574
Chromosome Location	chr6:44771041-44771042
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 144 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs1023091	0.83[ASN][1000 genomes]
rs10484627	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs10948185	0.86[CHD][hapmap]
rs10948187	0.84[CHD][hapmap]
rs10948188	0.84[CHD][hapmap]
rs10948190	0.84[CHD][hapmap]
rs10948194	0.84[CHD][hapmap]
rs10948197	0.84[CHD][hapmap]
rs12190136	0.81[ASN][1000 genomes]
rs12196818	0.82[CHD][hapmap]
rs12214778	0.84[CHD][hapmap]
rs12525773	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12526711	0.83[JPT][hapmap]
rs12526755	0.86[ASN][1000 genomes]
rs12527908	0.89[ASN][1000 genomes]
rs12529522	0.91[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs12530016	0.92[ASW][hapmap];0.86[CEU][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12661902	0.84[ASN][1000 genomes]
rs12663530	0.86[ASN][1000 genomes]
rs12663798	0.86[ASN][1000 genomes]
rs1293457	0.81[ASN][1000 genomes]
rs1293467	0.81[ASN][1000 genomes]
rs13199289	0.81[ASN][1000 genomes]
rs13202672	0.97[ASN][1000 genomes]
rs13206526	0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13216116	0.84[CHD][hapmap]
rs13216967	0.84[ASN][1000 genomes]
rs1329710	0.84[CHD][hapmap]
rs1329715	0.94[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1329716	0.86[CHD][hapmap]
rs13436998	0.84[YRI][hapmap]
rs1360195	0.94[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1402599	0.82[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1418435	0.85[ASN][1000 genomes]
rs1557143	0.81[ASN][1000 genomes]
rs16869119	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17422760	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs1891411	0.81[ASN][1000 genomes]
rs1891412	0.81[ASN][1000 genomes]
rs1935549	0.99[ASN][1000 genomes]
rs1935551	0.80[ASN][1000 genomes]
rs1980265	0.84[CHD][hapmap]
rs2139863	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs227857	0.84[ASN][1000 genomes]
rs2396369	0.84[CHD][hapmap]
rs2396372	0.86[CHD][hapmap]
rs2894599	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34243039	0.95[ASN][1000 genomes]
rs34286542	0.85[ASN][1000 genomes]
rs34776198	0.98[ASN][1000 genomes]
rs34817919	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35103634	0.86[ASN][1000 genomes]
rs35687006	0.94[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs35704584	0.86[ASN][1000 genomes]
rs35856781	0.95[ASN][1000 genomes]
rs35908738	0.85[ASN][1000 genomes]
rs36105034	0.85[ASN][1000 genomes]
rs3778507	0.84[CHD][hapmap]
rs3799965	0.93[CEU][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.98[ASN][1000 genomes]
rs3799966	0.97[ASN][1000 genomes]
rs3799967	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs3799969	0.98[ASN][1000 genomes]
rs3799970	0.98[ASN][1000 genomes]
rs3799971	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs3799972	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3799973	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs3799974	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3799976	0.83[JPT][hapmap]
rs3799977	0.84[CHD][hapmap];0.83[JPT][hapmap]
rs3799979	0.84[CHD][hapmap];0.83[JPT][hapmap]
rs3799984	0.83[JPT][hapmap]
rs3799986	0.84[CHD][hapmap]
rs3799987	0.94[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs3823252	0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3846896	0.80[ASN][1000 genomes]
rs3997503	0.86[ASN][1000 genomes]
rs4475320	0.86[ASN][1000 genomes]
rs4512220	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs4711799	0.81[ASN][1000 genomes]
rs4714812	0.80[CEU][hapmap];0.82[JPT][hapmap]
rs4714821	0.80[ASN][1000 genomes]
rs4714825	0.99[ASN][1000 genomes]
rs4714827	0.95[ASN][1000 genomes]
rs4714828	0.84[CHD][hapmap];0.83[JPT][hapmap]
rs4714829	0.86[ASN][1000 genomes]
rs4714830	0.84[CHD][hapmap]
rs4714834	0.83[ASN][1000 genomes]
rs494982	0.84[CHD][hapmap]
rs524492	0.92[ASW][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs542444	0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs562016	0.99[ASN][1000 genomes]
rs59945128	0.86[ASN][1000 genomes]
rs608941	0.84[CHD][hapmap]
rs609643	0.84[ASN][1000 genomes]
rs609699	0.84[ASN][1000 genomes]
rs636845	0.84[CHD][hapmap]
rs66642874	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67597621	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67911131	0.87[ASN][1000 genomes]
rs6904015	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs6904584	0.89[ASN][1000 genomes]
rs6910294	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs6910749	0.81[ASN][1000 genomes]
rs6919161	0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs720988	0.98[ASN][1000 genomes]
rs720989	0.96[ASN][1000 genomes]
rs72664272	0.96[ASN][1000 genomes]
rs72664273	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72664274	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746032	0.86[ASN][1000 genomes]
rs7749796	0.81[YRI][hapmap]
rs7751298	0.81[YRI][hapmap]
rs7754378	0.84[CHD][hapmap];0.83[JPT][hapmap]
rs7754698	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7769218	0.89[CEU][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs929614	0.81[ASN][1000 genomes]
rs9296450	0.85[ASW][hapmap];0.86[CEU][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9357459	0.81[ASN][1000 genomes]
rs9367211	0.82[JPT][hapmap]
rs9369512	0.81[ASN][1000 genomes]
rs9369513	0.80[ASN][1000 genomes]
rs9369514	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs9369516	0.84[CHD][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs9395051	0.84[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs9463017	0.85[ASN][1000 genomes]
rs9463039	0.95[ASN][1000 genomes]
rs9463040	0.95[ASN][1000 genomes]
rs9463046	0.81[YRI][hapmap]
rs9463056	0.81[YRI][hapmap]
rs9472331	0.80[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9472335	0.85[ASN][1000 genomes]
rs9472371	0.81[YRI][hapmap]
rs9472374	0.81[YRI][hapmap]
rs9472375	0.81[YRI][hapmap]
rs9472376	0.92[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472379	0.81[YRI][hapmap]
rs9472381	0.85[YRI][hapmap]
rs9472384	0.85[YRI][hapmap]
rs9472407	0.82[JPT][hapmap]
rs9472409	0.84[CHD][hapmap]
rs9472412	0.81[YRI][hapmap]
rs9472413	0.81[YRI][hapmap]
rs9472414	0.86[CEU][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.87[ASN][1000 genomes]
rs9885796	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16872574	SUPT3H	cis	multi-tissue	Pritchard
rs16872574	SUPT3H	cis	lymphoblastoid	seeQTL
rs16872574	UNC5CL	cis	cerebellum	SCAN
rs16872574	AARS2	cis	cerebellum	SCAN
rs16872574	MED20	cis	parietal	SCAN

Chromatin state (count:15 , 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	chr6:44768400-44772200	Weak transcription	Liver	Liver
3	chr6:44768600-44772600	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:44768800-44772200	Weak transcription	Fetal Intestine Small	intestine
5	chr6:44768800-44772400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:44768800-44773400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:44769000-44775400	Weak transcription	Pancreas	Pancrea
8	chr6:44769200-44772200	Weak transcription	Fetal Intestine Large	intestine
9	chr6:44769200-44776000	Weak transcription	Ovary	ovary
10	chr6:44769400-44772600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:44769400-44773000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:44769400-44774600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:44769600-44772800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:44769600-44773000	Weak transcription	Fetal Lung	lung
15	chr6:44769600-44774600	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links