Variant report

Variant	rs13193380
Chromosome Location	chr6:88297057-88297058
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	chr6:88296955-88297066	K562	blood:	n/a	n/a

Variant related genes	Relation type
ORC3	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1051131	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1051148	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10755484	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13194003	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2207146	0.81[EUR][1000 genomes]
rs2246113	0.83[EUR][1000 genomes]
rs2268993	0.82[EUR][1000 genomes]
rs2268994	0.82[EUR][1000 genomes]
rs2273129	0.81[EUR][1000 genomes]
rs2284908	0.81[EUR][1000 genomes]
rs2300906	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2300909	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2307379	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2325064	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2754247	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2754248	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2754260	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2754262	0.88[EUR][1000 genomes]
rs2787893	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2787921	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2787924	0.89[EUR][1000 genomes]
rs2814712	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3757368	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3934838	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4334949	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4464759	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4498321	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4587138	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4587143	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4706294	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4707373	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4707374	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4707376	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4707377	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4707379	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4707382	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4707383	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6454631	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6454632	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6454636	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6454638	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6454640	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6454641	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6906769	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6908386	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6916732	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6918909	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6923230	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6923355	0.81[EUR][1000 genomes]
rs6928160	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6930600	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6931069	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6940150	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7741825	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7742965	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7746465	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7750207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752494	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7754350	0.86[ASN][1000 genomes]
rs7755167	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7757636	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7757794	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7761814	0.80[EUR][1000 genomes]
rs7762864	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7772561	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7773906	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9444504	0.81[EUR][1000 genomes]
rs9444512	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9444519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9444522	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9444524	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9444525	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9444526	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9444530	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450712	0.81[EUR][1000 genomes]
rs9450723	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9450726	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450732	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9450733	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450738	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450739	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450744	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450762	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs985764	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv538354	chr6:88273858-88311606	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13193380	C6orf166	Cis_1M	lymphoblastoid	RTeQTL
rs13193380	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs13193380	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs13193380	SLC35A1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88227800-88298800	Weak transcription	Esophagus	oesophagus
2	chr6:88228400-88298400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:88256200-88297600	Weak transcription	Right Ventricle	heart
4	chr6:88272400-88297400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:88272400-88297400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:88273600-88298200	Weak transcription	Fetal Kidney	kidney
7	chr6:88274800-88298800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:88278800-88297400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:88283000-88298600	Weak transcription	Aorta	Aorta
10	chr6:88284400-88298000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:88284800-88298200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:88285200-88297400	Weak transcription	Brain Anterior Caudate	brain
13	chr6:88285400-88297200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr6:88285400-88297600	Weak transcription	Pancreas	Pancrea
15	chr6:88285600-88298200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:88286600-88297800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:88286800-88297800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:88289200-88297800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:88289200-88298600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr6:88289800-88298800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:88290000-88298000	Weak transcription	A549	lung
22	chr6:88290400-88298400	Weak transcription	Fetal Stomach	stomach
23	chr6:88290600-88297400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:88291000-88298000	Weak transcription	Thymus	Thymus
25	chr6:88291800-88298800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:88292400-88298200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr6:88292600-88297400	Weak transcription	Fetal Lung	lung
28	chr6:88292600-88297600	Weak transcription	Lung	lung
29	chr6:88292600-88297600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr6:88292600-88297800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:88292600-88297800	Weak transcription	HMEC	breast
32	chr6:88292600-88298000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:88292600-88298000	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:88292800-88297400	Weak transcription	NHEK	skin
35	chr6:88292800-88297600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:88292800-88297600	Weak transcription	NH-A	brain
37	chr6:88292800-88297800	Weak transcription	NHDF-Ad	bronchial
38	chr6:88292800-88298400	Weak transcription	HSMMtube	muscle
39	chr6:88293000-88297800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:88293000-88297800	Weak transcription	Osteobl	bone
41	chr6:88293000-88298000	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr6:88293200-88297400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr6:88293200-88298000	Weak transcription	HSMM	muscle
44	chr6:88293200-88298200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr6:88293400-88297400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:88293400-88298200	Weak transcription	Placenta	Placenta
47	chr6:88293800-88297400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:88293800-88298600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:88294000-88297800	Weak transcription	Brain Angular Gyrus	brain
50	chr6:88294000-88298000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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