Variant report

Variant	rs17339124
Chromosome Location	chr6:44942577-44942578
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 172 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:158)

rs_ID	r²[population]
rs1023089	0.81[ASN][1000 genomes]
rs1023090	0.81[ASN][1000 genomes]
rs1023091	0.84[ASN][1000 genomes]
rs1028944	0.82[ASN][1000 genomes]
rs1041332	0.80[ASN][1000 genomes]
rs1041333	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10456119	0.92[ASN][1000 genomes]
rs10484627	0.91[ASN][1000 genomes]
rs10948183	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10948185	0.94[ASN][1000 genomes]
rs10948186	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10948187	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10948188	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10948190	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10948193	0.98[ASN][1000 genomes]
rs10948194	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10948196	0.84[AFR][1000 genomes]
rs10948197	0.98[ASN][1000 genomes]
rs10948198	0.81[ASN][1000 genomes]
rs1150806	0.91[ASN][1000 genomes]
rs1159131	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11967188	0.98[ASN][1000 genomes]
rs12190513	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12191518	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12196818	0.98[ASN][1000 genomes]
rs12198904	0.89[ASN][1000 genomes]
rs12207620	0.88[ASN][1000 genomes]
rs12209076	0.89[ASN][1000 genomes]
rs12214778	0.98[ASN][1000 genomes]
rs12524069	0.94[ASN][1000 genomes]
rs12525009	0.91[ASN][1000 genomes]
rs12525773	0.87[ASN][1000 genomes]
rs12526711	0.91[ASN][1000 genomes]
rs12526755	0.87[ASN][1000 genomes]
rs12527908	0.84[ASN][1000 genomes]
rs12528232	0.84[ASN][1000 genomes]
rs12529522	0.82[ASN][1000 genomes]
rs12530016	0.83[ASN][1000 genomes]
rs12661902	0.85[ASN][1000 genomes]
rs12663530	0.81[ASN][1000 genomes]
rs12663798	0.87[ASN][1000 genomes]
rs1293598	0.90[ASN][1000 genomes]
rs1293600	0.84[ASN][1000 genomes]
rs13196587	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13199289	0.81[ASN][1000 genomes]
rs13202529	0.87[ASN][1000 genomes]
rs13203495	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13211229	0.99[ASN][1000 genomes]
rs13213412	0.89[ASN][1000 genomes]
rs13215618	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13216116	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329710	0.97[ASN][1000 genomes]
rs1329713	0.88[ASN][1000 genomes]
rs1329714	0.88[ASN][1000 genomes]
rs1329715	0.87[ASN][1000 genomes]
rs1329716	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1360195	0.87[ASN][1000 genomes]
rs1360197	0.95[ASN][1000 genomes]
rs1521355	0.98[ASN][1000 genomes]
rs1576382	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1578676	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1590864	0.94[ASN][1000 genomes]
rs17422760	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17424547	0.94[ASN][1000 genomes]
rs1831310	0.95[ASN][1000 genomes]
rs1854547	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1971482	0.88[ASN][1000 genomes]
rs1980265	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2396369	0.99[ASN][1000 genomes]
rs2396370	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2396371	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2396372	0.98[ASN][1000 genomes]
rs2396375	0.87[ASN][1000 genomes]
rs34286542	0.86[ASN][1000 genomes]
rs34808716	0.90[ASN][1000 genomes]
rs34982599	0.82[ASN][1000 genomes]
rs35103634	0.87[ASN][1000 genomes]
rs35357222	0.99[ASN][1000 genomes]
rs35687006	0.86[ASN][1000 genomes]
rs35704584	0.87[ASN][1000 genomes]
rs35813980	0.98[ASN][1000 genomes]
rs35908738	0.86[ASN][1000 genomes]
rs36105034	0.86[ASN][1000 genomes]
rs3778507	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3799971	0.86[ASN][1000 genomes]
rs3799973	0.86[ASN][1000 genomes]
rs3799976	0.90[ASN][1000 genomes]
rs3799977	0.89[ASN][1000 genomes]
rs3799979	0.89[ASN][1000 genomes]
rs3799981	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3799984	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3799986	0.94[ASN][1000 genomes]
rs3799987	0.87[ASN][1000 genomes]
rs3846896	0.90[ASN][1000 genomes]
rs3957281	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4398713	0.87[ASN][1000 genomes]
rs4475320	0.87[ASN][1000 genomes]
rs4512220	0.85[ASN][1000 genomes]
rs4711803	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4711805	0.90[ASN][1000 genomes]
rs4711807	0.99[ASN][1000 genomes]
rs4711809	0.84[ASN][1000 genomes]
rs4714828	0.88[ASN][1000 genomes]
rs4714829	0.87[ASN][1000 genomes]
rs4714830	0.98[ASN][1000 genomes]
rs4714832	0.95[ASN][1000 genomes]
rs4714834	0.84[ASN][1000 genomes]
rs472672	0.85[ASN][1000 genomes]
rs472673	0.83[ASN][1000 genomes]
rs494982	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs500773	0.90[ASN][1000 genomes]
rs538801	0.90[ASN][1000 genomes]
rs55893720	0.98[ASN][1000 genomes]
rs567054	0.81[ASN][1000 genomes]
rs588848	0.88[ASN][1000 genomes]
rs59945128	0.87[ASN][1000 genomes]
rs608941	0.91[ASN][1000 genomes]
rs62438007	0.89[ASN][1000 genomes]
rs636845	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6458414	0.87[ASN][1000 genomes]
rs6458415	0.90[ASN][1000 genomes]
rs67001335	0.88[ASN][1000 genomes]
rs67911131	0.82[ASN][1000 genomes]
rs679713	0.94[ASN][1000 genomes]
rs6903576	0.88[ASN][1000 genomes]
rs6904584	0.84[ASN][1000 genomes]
rs6919161	0.82[ASN][1000 genomes]
rs6919485	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6923519	0.90[ASN][1000 genomes]
rs6925017	0.98[ASN][1000 genomes]
rs6925467	0.87[ASN][1000 genomes]
rs718112	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7742360	0.87[ASN][1000 genomes]
rs7747642	0.88[ASN][1000 genomes]
rs7749865	0.98[ASN][1000 genomes]
rs7754378	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7763421	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7775717	0.97[ASN][1000 genomes]
rs865940	0.83[ASN][1000 genomes]
rs9296450	0.86[ASN][1000 genomes]
rs9357464	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9367208	0.81[ASN][1000 genomes]
rs9367211	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9369516	0.90[ASN][1000 genomes]
rs9369529	0.88[ASN][1000 genomes]
rs9381361	0.80[ASN][1000 genomes]
rs9395051	0.86[ASN][1000 genomes]
rs9395055	0.89[ASN][1000 genomes]
rs9395058	0.88[ASN][1000 genomes]
rs9463054	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9463055	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9472407	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9472409	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9472411	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472414	0.87[ASN][1000 genomes]
rs9472416	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs976699	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9885796	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17339124	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44919600-44943200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:44937400-44942800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:44937800-44943400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr6:44938200-44943600	Weak transcription	Primary T cells from cord blood	blood
5	chr6:44938800-44943400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr6:44939800-44942600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:44939800-44951200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:44940800-44957000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:44941000-44944800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:44941200-44942600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:44941600-44947000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr6:44942000-44943800	Weak transcription	Dnd41	blood
13	chr6:44942000-44944800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:44942200-44942600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:44942200-44946400	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr6:44942200-44947000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr6:44942400-44943000	Enhancers	Fetal Heart	heart
18	chr6:44942400-44944600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:44942400-44945000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:44942400-44946600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr6:44942400-44946800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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