Variant report

Variant	rs6938741
Chromosome Location	chr6:109873277-109873278
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:109872667-109873951	K562	blood:	n/a	n/a

Variant related genes	Relation type
AK9	TF binding region

Extended variants
information (count: 130 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10457201	0.82[EUR][1000 genomes]
rs10872041	0.84[EUR][1000 genomes]
rs10872047	0.82[EUR][1000 genomes]
rs1096136	0.85[EUR][1000 genomes]
rs1096138	0.90[EUR][1000 genomes]
rs1115977	0.81[EUR][1000 genomes]
rs11753828	0.82[EUR][1000 genomes]
rs11754263	0.83[EUR][1000 genomes]
rs11966009	0.84[EUR][1000 genomes]
rs12200787	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12524352	0.81[EUR][1000 genomes]
rs1358759	0.81[EUR][1000 genomes]
rs1474959	0.81[EUR][1000 genomes]
rs1570011	0.83[EUR][1000 genomes]
rs1570012	0.82[EUR][1000 genomes]
rs1590187	0.81[EUR][1000 genomes]
rs17540056	0.82[EUR][1000 genomes]
rs1925921	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1967725	0.81[EUR][1000 genomes]
rs1969710	0.80[EUR][1000 genomes]
rs1969711	0.81[EUR][1000 genomes]
rs1985123	0.81[EUR][1000 genomes]
rs1998812	0.82[EUR][1000 genomes]
rs2064820	0.84[EUR][1000 genomes]
rs2064822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2357123	0.84[EUR][1000 genomes]
rs2357125	0.82[EUR][1000 genomes]
rs2357127	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4296926	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4523125	0.81[EUR][1000 genomes]
rs4946982	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4946986	0.84[EUR][1000 genomes]
rs4946987	0.84[EUR][1000 genomes]
rs4946989	0.82[EUR][1000 genomes]
rs4946992	0.81[EUR][1000 genomes]
rs4946995	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4946997	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4946998	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4947004	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4947006	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs56125306	0.86[EUR][1000 genomes]
rs56264193	0.85[EUR][1000 genomes]
rs62437563	0.82[EUR][1000 genomes]
rs6568579	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6568580	0.81[EUR][1000 genomes]
rs6568582	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6568583	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6568591	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6568601	0.82[EUR][1000 genomes]
rs67715693	0.84[EUR][1000 genomes]
rs6900133	0.83[EUR][1000 genomes]
rs6900187	0.81[EUR][1000 genomes]
rs6911851	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6912368	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6916239	0.82[EUR][1000 genomes]
rs6917300	0.83[EUR][1000 genomes]
rs6921303	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6924436	0.83[EUR][1000 genomes]
rs6925886	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6929823	0.83[EUR][1000 genomes]
rs6931630	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6932774	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6942171	0.82[EUR][1000 genomes]
rs7453835	0.81[EUR][1000 genomes]
rs7454678	0.80[EUR][1000 genomes]
rs7749386	0.81[EUR][1000 genomes]
rs7754118	0.81[EUR][1000 genomes]
rs7754606	0.81[EUR][1000 genomes]
rs7771729	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7772109	0.82[EUR][1000 genomes]
rs7773915	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7775420	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs829817	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs911022	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs911023	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9320290	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9320294	0.83[EUR][1000 genomes]
rs9320295	0.83[EUR][1000 genomes]
rs9320296	0.83[EUR][1000 genomes]
rs9320299	0.83[EUR][1000 genomes]
rs9320300	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9320304	0.81[EUR][1000 genomes]
rs9320305	0.81[EUR][1000 genomes]
rs9372216	0.81[EUR][1000 genomes]
rs9372220	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9374092	0.80[EUR][1000 genomes]
rs9374095	0.84[EUR][1000 genomes]
rs9374096	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9374097	0.84[EUR][1000 genomes]
rs9374098	0.81[EUR][1000 genomes]
rs9374099	0.84[EUR][1000 genomes]
rs9374108	0.81[EUR][1000 genomes]
rs9384713	0.84[EUR][1000 genomes]
rs9384715	0.83[EUR][1000 genomes]
rs9384716	0.82[EUR][1000 genomes]
rs9386812	0.84[EUR][1000 genomes]
rs9386813	0.84[EUR][1000 genomes]
rs9386814	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9386816	0.81[EUR][1000 genomes]
rs9386818	0.81[EUR][1000 genomes]
rs9386823	0.81[EUR][1000 genomes]
rs9386824	0.81[EUR][1000 genomes]
rs9386825	0.81[EUR][1000 genomes]
rs9398204	0.82[EUR][1000 genomes]
rs9398206	0.82[EUR][1000 genomes]
rs9400289	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9400291	0.84[EUR][1000 genomes]
rs9400294	0.84[EUR][1000 genomes]
rs9400295	0.84[EUR][1000 genomes]
rs9400300	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9400301	0.81[EUR][1000 genomes]
rs942923	0.81[EUR][1000 genomes]
rs942924	0.82[EUR][1000 genomes]
rs9480973	0.84[EUR][1000 genomes]
rs9480974	0.84[EUR][1000 genomes]
rs9480976	0.84[EUR][1000 genomes]
rs9480982	0.81[EUR][1000 genomes]
rs9487141	0.84[EUR][1000 genomes]
rs9487148	0.84[EUR][1000 genomes]
rs9487152	0.81[EUR][1000 genomes]
rs9487156	0.82[EUR][1000 genomes]
rs9487160	0.81[EUR][1000 genomes]
rs9487170	0.81[EUR][1000 genomes]
rs9487171	0.81[EUR][1000 genomes]
rs9968792	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9986507	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026012	chr6:109851638-109999379	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv604484	chr6:109851937-109997529	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1019389	chr6:109868058-109987502	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv538416	chr6:109868058-109987502	Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6938741	SMPD2	cis	Whole Blood	GTEx
rs6938741	C6orf199	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109852200-109878400	Weak transcription	Pancreas	Pancrea
2	chr6:109862200-109878200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:109862200-109878400	Weak transcription	Thymus	Thymus
4	chr6:109867000-109885800	Weak transcription	Ovary	ovary
5	chr6:109870600-109878400	Weak transcription	Left Ventricle	heart
6	chr6:109870600-109878800	Weak transcription	Primary T cells from cord blood	blood
7	chr6:109871400-109884000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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