Variant report

Variant	rs9395049
Chromosome Location	chr6:44792718-44792719
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:44791441..44794035-chr6:44828458..44830596,2	K562	blood:
2	chr6:44788604..44791132-chr6:44792129..44794044,2	K562	blood:

Extended variants
information (count: 132 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1023091	0.84[CHB][hapmap]
rs1028944	0.84[CHB][hapmap]
rs10456119	0.82[ASN][1000 genomes]
rs10484627	0.89[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs10948183	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs10948185	0.95[CHB][hapmap]
rs10948186	0.89[CEU][hapmap];0.94[CHB][hapmap]
rs10948187	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[TSI][hapmap]
rs10948188	0.94[CHB][hapmap]
rs10948190	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[TSI][hapmap]
rs10948194	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs10948197	0.95[CHB][hapmap]
rs11967188	0.94[CHB][hapmap]
rs12190136	0.97[ASN][1000 genomes]
rs12190513	0.94[CHB][hapmap]
rs12192367	0.94[CHB][hapmap];0.93[ASN][1000 genomes]
rs12196818	0.95[CHB][hapmap]
rs12198904	0.81[ASN][1000 genomes]
rs12207620	0.81[ASN][1000 genomes]
rs12209076	0.84[ASN][1000 genomes]
rs12214778	0.95[CHB][hapmap]
rs12525009	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs12526711	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs12528232	0.84[CHB][hapmap]
rs1293457	0.97[ASN][1000 genomes]
rs1293467	0.97[ASN][1000 genomes]
rs13199289	0.84[ASN][1000 genomes]
rs13213412	0.82[ASN][1000 genomes]
rs13215618	0.94[CHB][hapmap]
rs13216116	0.95[CHB][hapmap]
rs1329710	0.82[CEU][hapmap];0.95[CHB][hapmap];0.80[MEX][hapmap]
rs1329715	0.84[CHB][hapmap]
rs1329716	0.89[CEU][hapmap];0.90[CHB][hapmap];0.81[TSI][hapmap]
rs1342370	0.93[ASN][1000 genomes]
rs1360195	0.84[CHB][hapmap]
rs1360197	0.81[CEU][hapmap];0.95[CHB][hapmap]
rs1418434	0.93[ASN][1000 genomes]
rs1521355	0.81[CEU][hapmap];0.95[CHB][hapmap]
rs1557143	0.97[ASN][1000 genomes]
rs17422760	0.89[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs17424547	0.95[CHB][hapmap]
rs1891411	0.97[ASN][1000 genomes]
rs1891412	0.97[ASN][1000 genomes]
rs1935551	0.98[ASN][1000 genomes]
rs1971482	0.95[CHB][hapmap]
rs1980265	0.89[CEU][hapmap];0.90[CHB][hapmap];0.81[TSI][hapmap]
rs2038555	0.91[ASN][1000 genomes]
rs2038556	0.93[ASN][1000 genomes]
rs2038557	0.93[ASN][1000 genomes]
rs2040032	0.93[ASN][1000 genomes]
rs227849	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap]
rs2396369	0.95[CHB][hapmap]
rs2396371	0.96[CEU][hapmap];0.89[CHB][hapmap]
rs2396372	0.95[CHB][hapmap]
rs2396373	0.82[CEU][hapmap]
rs34808716	0.82[ASN][1000 genomes]
rs35687006	0.84[CHB][hapmap]
rs3778507	0.89[CEU][hapmap];0.90[CHB][hapmap];0.81[TSI][hapmap]
rs3799965	0.83[CHB][hapmap]
rs3799967	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs3799968	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]
rs3799971	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs3799973	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3799976	0.95[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs3799977	0.95[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs3799979	0.95[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs3799981	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs3799984	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs3799986	0.88[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.80[MEX][hapmap]
rs3799987	0.84[CHB][hapmap]
rs3846896	0.83[ASN][1000 genomes]
rs3957281	0.81[ASN][1000 genomes]
rs4512220	0.84[CHB][hapmap]
rs4711798	0.93[ASN][1000 genomes]
rs4711799	0.97[ASN][1000 genomes]
rs4711803	0.82[ASN][1000 genomes]
rs4711805	0.82[ASN][1000 genomes]
rs4711807	0.95[CHB][hapmap]
rs4711809	0.94[CHB][hapmap]
rs4714819	0.91[ASN][1000 genomes]
rs4714820	0.91[ASN][1000 genomes]
rs4714821	0.90[ASN][1000 genomes]
rs4714822	0.93[ASN][1000 genomes]
rs4714828	0.95[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4714830	0.95[CHB][hapmap];0.82[GIH][hapmap]
rs4714834	0.84[CHB][hapmap]
rs494982	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[TSI][hapmap]
rs500773	0.82[ASN][1000 genomes]
rs538801	0.82[CEU][hapmap];0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs588848	0.81[ASN][1000 genomes]
rs59881382	0.82[ASN][1000 genomes]
rs608941	0.95[CHB][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs62438007	0.81[ASN][1000 genomes]
rs636845	0.89[CEU][hapmap];0.90[CHB][hapmap];0.81[TSI][hapmap]
rs6458415	0.96[CEU][hapmap];0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs6904015	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs6910294	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs6910749	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6919161	0.84[CHB][hapmap]
rs6925017	0.94[CHB][hapmap]
rs718112	0.81[ASN][1000 genomes]
rs764396	0.82[ASN][1000 genomes]
rs764397	0.82[ASN][1000 genomes]
rs7749865	0.94[CHB][hapmap]
rs7754378	0.90[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7754698	0.94[CHB][hapmap];0.87[JPT][hapmap];0.97[ASN][1000 genomes]
rs7763421	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs7769218	0.82[CHB][hapmap]
rs7775717	0.95[CHB][hapmap]
rs929614	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9349303	0.89[CEU][hapmap]
rs9357459	0.97[ASN][1000 genomes]
rs9357464	0.96[CEU][hapmap];0.94[CHB][hapmap]
rs9367208	0.85[ASN][1000 genomes]
rs9367211	0.96[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs9369512	0.97[ASN][1000 genomes]
rs9369513	0.98[ASN][1000 genomes]
rs9369514	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.98[ASN][1000 genomes]
rs9369516	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs9369523	0.82[CEU][hapmap]
rs9381359	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs9395051	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs9472336	0.82[ASN][1000 genomes]
rs9472339	0.82[ASN][1000 genomes]
rs9472360	0.93[ASN][1000 genomes]
rs9472383	0.81[ASN][1000 genomes]
rs9472407	0.89[CHB][hapmap]
rs9472409	0.90[CHB][hapmap]
rs9472416	0.89[CHB][hapmap]
rs9472418	0.89[CEU][hapmap]
rs976699	1.00[CEU][hapmap];0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1842105	chr6:44783457-44798701	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9395049	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL
rs9395049	SUPT3H	cis	lymphoblastoid	seeQTL
rs9395049	SUPT3H	cis	multi-tissue	Pritchard
rs9395049	C6orf226	cis	cerebellum	SCAN
rs9395049	SUPT3H	cis	cerebellum	SCAN
rs9395049	SUPT3H	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44777400-44796600	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr6:44779600-44796200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:44779600-44796600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:44779600-44796800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:44779600-44796800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:44780000-44798400	Weak transcription	Dnd41	blood
7	chr6:44785200-44795200	Weak transcription	Aorta	Aorta
8	chr6:44785200-44796800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr6:44785800-44796400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr6:44786200-44797200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:44789200-44794600	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr6:44789200-44796800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr6:44790400-44797200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:44791000-44793600	Weak transcription	Fetal Stomach	stomach
15	chr6:44791000-44805600	Weak transcription	Ovary	ovary
16	chr6:44791200-44796400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr6:44791200-44799000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:44791800-44792800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr6:44791800-44792800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr6:44791800-44794200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr6:44792000-44811600	Weak transcription	Pancreas	Pancrea
22	chr6:44792200-44792800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr6:44792200-44796600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr6:44792400-44793800	Enhancers	Fetal Intestine Large	intestine
25	chr6:44792400-44796800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:44792600-44792800	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr6:44792600-44793400	Enhancers	H9 Cell Line	embryonic stem cell
28	chr6:44792600-44796200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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