Variant report

Variant	rs55893720
Chromosome Location	chr6:44955716-44955717
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 198 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:183)

rs_ID	r²[population]
rs1023089	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1023090	0.81[ASN][1000 genomes]
rs1023091	0.85[ASN][1000 genomes]
rs1028944	0.83[ASN][1000 genomes]
rs1041332	0.82[ASN][1000 genomes]
rs1041333	0.95[ASN][1000 genomes]
rs10456119	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10484627	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10948183	0.91[ASN][1000 genomes]
rs10948185	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10948186	0.94[ASN][1000 genomes]
rs10948187	0.97[ASN][1000 genomes]
rs10948188	0.98[ASN][1000 genomes]
rs10948190	0.98[ASN][1000 genomes]
rs10948192	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10948193	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948194	0.98[ASN][1000 genomes]
rs10948197	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10948198	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1150806	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1159131	0.91[ASN][1000 genomes]
rs11967188	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968042	0.81[EUR][1000 genomes]
rs12190261	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12190513	0.98[ASN][1000 genomes]
rs12191518	0.93[ASN][1000 genomes]
rs12196818	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12198904	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12205071	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12207620	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12208023	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12208339	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12208483	0.81[EUR][1000 genomes]
rs12209076	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12214778	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12524069	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12525009	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12525773	0.86[ASN][1000 genomes]
rs12526711	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12526755	0.87[ASN][1000 genomes]
rs12527908	0.83[ASN][1000 genomes]
rs12528232	0.85[ASN][1000 genomes]
rs12529490	0.80[EUR][1000 genomes]
rs12529522	0.82[ASN][1000 genomes]
rs12530016	0.81[ASN][1000 genomes]
rs12661902	0.85[ASN][1000 genomes]
rs12663530	0.81[ASN][1000 genomes]
rs12663798	0.87[ASN][1000 genomes]
rs1284972	0.81[EUR][1000 genomes]
rs1284973	0.82[EUR][1000 genomes]
rs1284975	0.82[EUR][1000 genomes]
rs1284982	0.82[EUR][1000 genomes]
rs1284983	0.82[EUR][1000 genomes]
rs1284988	0.82[EUR][1000 genomes]
rs1284992	0.82[EUR][1000 genomes]
rs1293598	0.88[ASN][1000 genomes]
rs1293600	0.83[ASN][1000 genomes]
rs13196587	0.98[ASN][1000 genomes]
rs13199289	0.81[ASN][1000 genomes]
rs13202529	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13203495	0.97[ASN][1000 genomes]
rs13207575	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13211229	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13213412	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13215618	0.90[ASN][1000 genomes]
rs13216116	0.98[ASN][1000 genomes]
rs1324532	0.82[EUR][1000 genomes]
rs1329710	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1329713	0.88[ASN][1000 genomes]
rs1329714	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1329715	0.87[ASN][1000 genomes]
rs1329716	0.98[ASN][1000 genomes]
rs1360195	0.87[ASN][1000 genomes]
rs1360197	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1521355	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1576382	0.98[ASN][1000 genomes]
rs1578676	0.94[ASN][1000 genomes]
rs1590864	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17339124	0.98[ASN][1000 genomes]
rs17422760	0.90[ASN][1000 genomes]
rs17424547	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1831310	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1854547	0.98[ASN][1000 genomes]
rs1937046	0.81[EUR][1000 genomes]
rs1937047	0.81[EUR][1000 genomes]
rs1971482	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1980265	0.97[ASN][1000 genomes]
rs2186062	0.84[EUR][1000 genomes]
rs2396369	0.98[ASN][1000 genomes]
rs2396370	0.98[ASN][1000 genomes]
rs2396371	0.98[ASN][1000 genomes]
rs2396372	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396375	0.88[ASN][1000 genomes]
rs34286542	0.87[ASN][1000 genomes]
rs34808716	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34982599	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35103634	0.87[ASN][1000 genomes]
rs35357222	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35687006	0.87[ASN][1000 genomes]
rs35704584	0.87[ASN][1000 genomes]
rs35813980	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35908738	0.86[ASN][1000 genomes]
rs36105034	0.87[ASN][1000 genomes]
rs3778507	0.93[ASN][1000 genomes]
rs3799971	0.84[ASN][1000 genomes]
rs3799973	0.86[ASN][1000 genomes]
rs3799976	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3799977	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3799979	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3799981	0.90[ASN][1000 genomes]
rs3799984	0.90[ASN][1000 genomes]
rs3799986	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3799987	0.87[ASN][1000 genomes]
rs3846896	0.88[ASN][1000 genomes]
rs3957281	0.89[ASN][1000 genomes]
rs4398713	0.89[ASN][1000 genomes]
rs4412189	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4475320	0.87[ASN][1000 genomes]
rs4512220	0.85[ASN][1000 genomes]
rs4711803	0.90[ASN][1000 genomes]
rs4711805	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4711807	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711809	0.85[ASN][1000 genomes]
rs4714828	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4714829	0.87[ASN][1000 genomes]
rs4714830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714832	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4714834	0.85[ASN][1000 genomes]
rs4714836	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs472672	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs472673	0.83[ASN][1000 genomes]
rs494982	0.98[ASN][1000 genomes]
rs500773	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs538801	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs588848	0.88[ASN][1000 genomes]
rs59945128	0.87[ASN][1000 genomes]
rs608941	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62438007	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs636845	0.98[ASN][1000 genomes]
rs6458414	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6458415	0.88[ASN][1000 genomes]
rs6458418	0.85[EUR][1000 genomes]
rs67001335	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs67911131	0.82[ASN][1000 genomes]
rs679713	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6903576	0.87[ASN][1000 genomes]
rs6904584	0.83[ASN][1000 genomes]
rs6919161	0.82[ASN][1000 genomes]
rs6919485	0.97[ASN][1000 genomes]
rs6923436	0.81[EUR][1000 genomes]
rs6923519	0.88[ASN][1000 genomes]
rs6925017	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6925467	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs718112	0.90[ASN][1000 genomes]
rs7742360	0.89[ASN][1000 genomes]
rs7747642	0.88[ASN][1000 genomes]
rs7749865	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7754378	0.90[ASN][1000 genomes]
rs7758031	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7763421	0.90[ASN][1000 genomes]
rs7763450	0.84[EUR][1000 genomes]
rs7764102	0.82[EUR][1000 genomes]
rs7775717	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs865940	0.83[ASN][1000 genomes]
rs9296450	0.86[ASN][1000 genomes]
rs9357464	0.98[ASN][1000 genomes]
rs9367211	0.89[ASN][1000 genomes]
rs9369516	0.88[ASN][1000 genomes]
rs9369529	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9381361	0.82[ASN][1000 genomes]
rs9395051	0.84[ASN][1000 genomes]
rs9395055	0.87[ASN][1000 genomes]
rs9395058	0.90[ASN][1000 genomes]
rs9463054	0.97[ASN][1000 genomes]
rs9463055	0.96[ASN][1000 genomes]
rs9472407	0.94[ASN][1000 genomes]
rs9472409	0.98[ASN][1000 genomes]
rs9472411	0.98[ASN][1000 genomes]
rs9472414	0.86[ASN][1000 genomes]
rs9472416	0.98[ASN][1000 genomes]
rs969211	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs976699	0.98[ASN][1000 genomes]
rs9885796	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885861	chr6:44837356-45043618	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv1024370	chr6:44878053-45251451	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	esv2758051	chr6:44879791-45056758	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv2759423	chr6:44879791-45056758	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv885862	chr6:44890760-45083966	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv885863	chr6:44890760-45083966	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv885864	chr6:44890760-45198796	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
10	nsv462938	chr6:44909515-45008779	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv470817	chr6:44909515-45008779	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv603007	chr6:44909515-45008779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1023018	chr6:44925393-45152912	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv538212	chr6:44925393-45152912	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	esv2757164	chr6:44953758-44989519	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55893720	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44940800-44957000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:44947800-44962000	Weak transcription	Pancreas	Pancrea
3	chr6:44951200-44980800	Weak transcription	Aorta	Aorta
4	chr6:44955000-44955800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr6:44955000-44955800	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr6:44955000-44955800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr6:44955200-44956000	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr6:44955600-44968400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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