Variant report

Variant	rs8078686
Chromosome Location	chr17:45735706-45735707
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10853090	0.86[EUR][1000 genomes]
rs11079784	0.88[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs11650372	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11656855	0.86[EUR][1000 genomes]
rs11870935	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11871606	0.88[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs12150231	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12943464	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs16942199	0.90[CHB][hapmap]
rs2317826	0.94[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3760370	0.88[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs3809868	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4239162	0.88[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs4239163	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs4264433	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4289035	0.88[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs4375701	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4399567	0.86[EUR][1000 genomes]
rs4439799	0.81[CEU][hapmap]
rs4580230	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4793842	0.84[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs4793908	0.80[EUR][1000 genomes]
rs4793978	0.85[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs4794001	0.88[CEU][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs4794016	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794047	0.81[CEU][hapmap];0.90[CHB][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4794048	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4794058	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs55633793	0.83[EUR][1000 genomes]
rs56226803	0.87[EUR][1000 genomes]
rs7210738	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7219303	0.87[EUR][1000 genomes]
rs7220935	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7223029	0.83[EUR][1000 genomes]
rs73315878	0.86[EUR][1000 genomes]
rs8065437	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8065669	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8072100	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8072644	0.88[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs8075411	0.88[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs8078880	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs9635762	0.87[CEU][hapmap]
rs9905583	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9905922	0.86[EUR][1000 genomes]
rs9912311	0.81[CEU][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv525267	chr17:45451894-45735706	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv1811231	chr17:45520374-45764956	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv1813964	chr17:45520374-45764956	Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv2758458	chr17:45520374-45764956	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv2758693	chr17:45520374-45764956	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv428344	chr17:45520374-45764956	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs8078686	DBF4B	cis	cerebellum	SCAN
rs8078686	NPEPPS	cis	parietal	SCAN
rs8078686	KLHL11	cis	cerebellum	SCAN
rs8078686	MRPL45P2	cis	Skin Sun Exposed Lower leg	GTEx
rs8078686	MRPL45P2	cis	lymphoblastoid	seeQTL
rs8078686	TBKBP1	cis	Nerve Tibial	GTEx
rs8078686	VPS25	cis	cerebellum	SCAN
rs8078686	TBKBP1	cis	Artery Tibial	GTEx
rs8078686	CDK5RAP3	cis	cerebellum	SCAN
rs8078686	SLC25A39	cis	parietal	SCAN
rs8078686	VPS25	cis	parietal	SCAN
rs8078686	RAB5C	cis	parietal	SCAN
rs8078686	C17orf57	cis	parietal	SCAN
rs8078686	C17orf57	cis	cerebellum	SCAN
rs8078686	KPNB1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45728800-45742400	Strong transcription	H9 Cell Line	embryonic stem cell
2	chr17:45728800-45744600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr17:45728800-45762800	Strong transcription	Fetal Stomach	stomach
4	chr17:45728800-45765600	Strong transcription	Fetal Muscle Trunk	muscle
5	chr17:45729000-45743400	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr17:45729200-45736600	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr17:45729200-45736800	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr17:45729200-45760400	Strong transcription	Fetal Muscle Leg	muscle
9	chr17:45729200-45760600	Strong transcription	Fetal Brain Female	brain
10	chr17:45729200-45763800	Strong transcription	Placenta	Placenta
11	chr17:45729400-45736400	Strong transcription	Colonic Mucosa	Colon
12	chr17:45729400-45737400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
13	chr17:45729400-45741800	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr17:45729600-45736600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr17:45729600-45737000	Strong transcription	Thymus	Thymus
16	chr17:45729600-45742200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:45729600-45762600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr17:45729800-45752000	Strong transcription	Left Ventricle	heart
19	chr17:45729800-45761600	Strong transcription	HSMM	muscle
20	chr17:45730000-45736200	Strong transcription	Primary hematopoietic stem cells	blood
21	chr17:45730000-45736600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr17:45730000-45739600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr17:45730000-45740000	Strong transcription	Aorta	Aorta
24	chr17:45730000-45741000	Strong transcription	HSMMtube	muscle
25	chr17:45730000-45741600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr17:45730200-45736200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr17:45730200-45736200	Strong transcription	Fetal Thymus	thymus
28	chr17:45730200-45741400	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr17:45730400-45737400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
30	chr17:45730400-45741600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr17:45730400-45764800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr17:45730400-45765000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr17:45730600-45741000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
34	chr17:45730600-45741800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr17:45730800-45736000	Strong transcription	Ovary	ovary
36	chr17:45730800-45736800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr17:45730800-45760600	Strong transcription	Lung	lung
38	chr17:45731000-45736200	Strong transcription	Primary B cells from cord blood	blood
39	chr17:45731000-45736400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr17:45731000-45757600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr17:45731200-45741000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr17:45731200-45762200	Strong transcription	Fetal Lung	lung
43	chr17:45731200-45763800	Strong transcription	K562	blood
44	chr17:45731400-45737400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr17:45731400-45737600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr17:45731400-45740800	Strong transcription	Fetal Kidney	kidney
47	chr17:45731400-45741600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr17:45731400-45744600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr17:45731400-45762000	Strong transcription	NH-A	brain
50	chr17:45731800-45736600	Strong transcription	Spleen	Spleen

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