Variant report

Variant	rs3799968
Chromosome Location	chr6:44805377-44805378
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	chr6:44797166..44798677-chr6:44803653..44805802,3	K562	blood:
2	chr6:44804801..44806639-chr6:44808524..44811401,2	K562	blood:

Extended variants
information (count: 140 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs1041333	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10484627	0.84[CHB][hapmap]
rs10948183	0.95[CHB][hapmap]
rs10948185	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs10948186	0.92[CEU][hapmap];0.89[CHB][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10948187	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10948188	0.89[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs10948190	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10948194	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10948195	0.85[EUR][1000 genomes]
rs10948197	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs1159131	0.85[TSI][hapmap]
rs11967188	0.88[CHB][hapmap]
rs12190136	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12190513	0.94[CHB][hapmap]
rs12191518	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12192367	1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs12196818	0.89[CHB][hapmap]
rs12214778	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs12525009	0.84[CHB][hapmap]
rs12526711	0.82[CHB][hapmap]
rs1293457	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1293467	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1293598	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1293600	0.80[EUR][1000 genomes]
rs13215618	1.00[CHB][hapmap]
rs13216116	0.89[CHB][hapmap];0.81[CHD][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs1329710	0.81[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap]
rs1329713	0.94[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs1329714	0.93[CHB][hapmap]
rs1329716	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1342370	0.90[ASN][1000 genomes]
rs1360196	0.85[EUR][1000 genomes]
rs1360197	0.80[CEU][hapmap];0.89[CHB][hapmap]
rs1418434	0.90[ASN][1000 genomes]
rs1521355	0.89[CHB][hapmap]
rs1557143	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1576382	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17422760	0.84[CHB][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs17424547	0.89[CHB][hapmap]
rs1854547	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1891411	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1891412	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1935551	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1971482	0.89[CHB][hapmap]
rs1980265	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2038555	0.88[ASN][1000 genomes]
rs2038556	0.90[ASN][1000 genomes]
rs2038557	0.90[ASN][1000 genomes]
rs2040032	0.90[ASN][1000 genomes]
rs2145826	0.84[EUR][1000 genomes]
rs227849	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes]
rs227850	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs227851	0.81[CEU][hapmap]
rs227852	0.89[CHD][hapmap]
rs227853	0.89[CHD][hapmap]
rs227855	0.80[CEU][hapmap]
rs2396369	0.89[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap]
rs2396370	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2396371	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2396372	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs2396373	0.85[CEU][hapmap]
rs3778507	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3799967	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3799971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3799973	0.94[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs3799976	0.89[CHB][hapmap]
rs3799977	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs3799978	0.88[EUR][1000 genomes]
rs3799979	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs3799981	0.89[CHB][hapmap]
rs3799984	0.89[CHB][hapmap]
rs3799986	0.81[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap]
rs3846896	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4398713	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs4711798	0.90[ASN][1000 genomes]
rs4711799	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4711803	0.81[AMR][1000 genomes]
rs4711807	0.89[CHB][hapmap]
rs4711809	0.89[CHB][hapmap]
rs4714812	0.89[CHD][hapmap]
rs4714819	0.88[ASN][1000 genomes]
rs4714820	0.88[ASN][1000 genomes]
rs4714821	0.87[ASN][1000 genomes]
rs4714822	0.90[ASN][1000 genomes]
rs4714828	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs4714830	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs494982	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs538801	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs567054	0.82[EUR][1000 genomes]
rs57020561	0.87[EUR][1000 genomes]
rs608941	0.89[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap]
rs636845	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6458415	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6903576	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6904015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6910294	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6910749	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6919485	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6923519	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6925017	0.88[CHB][hapmap]
rs6925467	0.89[CHB][hapmap]
rs6940547	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs718112	0.81[AMR][1000 genomes]
rs7742360	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs7749865	0.89[CHB][hapmap]
rs7754378	0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs7754698	1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7775717	0.89[CHB][hapmap]
rs929614	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9296448	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9296450	0.84[CHB][hapmap]
rs9349303	0.92[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs9357459	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9357464	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9367208	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9367211	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9369512	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9369513	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9369514	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9369515	0.94[EUR][1000 genomes]
rs9369516	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9369519	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9369523	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs9369529	0.89[CHB][hapmap]
rs9381359	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs9395049	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs9395051	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9395055	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9463054	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9463055	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9472360	0.90[ASN][1000 genomes]
rs9472383	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9472403	0.88[EUR][1000 genomes]
rs9472407	0.94[CHB][hapmap]
rs9472409	0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs9472414	0.84[CHB][hapmap]
rs9472416	0.94[CHB][hapmap]
rs9472418	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs976699	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3799968	SUPT3H	cis	cerebellum	SCAN
rs3799968	SUPT3H	cis	parietal	SCAN
rs3799968	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL
rs3799968	MAD2L1BP	cis	cerebellum	SCAN
rs3799968	SUPT3H	cis	lymphoblastoid	seeQTL
rs3799968	C6orf226	cis	cerebellum	SCAN

Chromatin state (count:10 , 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	chr6:44798200-44811200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:44798400-44822800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:44798600-44810600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr6:44799200-44806000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:44804200-44809600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:44804800-44806200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:44804800-44806400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr6:44805200-44805800	Enhancers	Primary monocytes fromperipheralblood	blood

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