Variant report

Variant	rs4793978
Chromosome Location	chr17:45698175-45698176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45697869..45699408-chr17:45722972..45724595,2	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10163469	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10853090	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11079782	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11079783	0.86[LWK][hapmap];0.81[TSI][hapmap]
rs11079784	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1138193	0.88[ASN][1000 genomes]
rs11650372	0.95[EUR][1000 genomes]
rs11656855	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870935	0.85[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs11871606	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12150231	0.95[EUR][1000 genomes]
rs12603290	0.84[EUR][1000 genomes]
rs12936468	0.97[ASN][1000 genomes]
rs12937560	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12943464	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1962307	0.81[TSI][hapmap]
rs2125873	0.80[ASN][1000 genomes]
rs2317826	0.89[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs35919601	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3760370	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760371	0.86[LWK][hapmap];0.81[TSI][hapmap]
rs3809868	0.89[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs3865314	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4092460	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4239162	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4239163	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4264433	0.85[EUR][1000 genomes]
rs4289035	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4375701	0.93[EUR][1000 genomes]
rs4399567	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4580230	0.91[EUR][1000 genomes]
rs4793836	0.91[ASN][1000 genomes]
rs4793842	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4793908	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4793913	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4794001	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4794016	0.94[EUR][1000 genomes]
rs4794047	0.82[TSI][hapmap]
rs4794048	0.89[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs4794058	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs55633793	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56226803	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62074014	0.80[EUR][1000 genomes]
rs62074015	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6503796	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs6505049	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7207542	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7210738	0.89[CEU][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs7213086	0.96[ASN][1000 genomes]
rs7214799	0.81[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7219303	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7220935	0.97[EUR][1000 genomes]
rs7222225	0.86[LWK][hapmap];0.81[TSI][hapmap]
rs7223029	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73315878	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8065437	0.95[EUR][1000 genomes]
rs8065669	0.89[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs8070463	0.81[CEU][hapmap];0.86[CHD][hapmap]
rs8070759	0.84[EUR][1000 genomes]
rs8072100	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs8072644	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8075411	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8077106	0.83[EUR][1000 genomes]
rs8078686	0.85[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs8078880	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8081717	0.83[EUR][1000 genomes]
rs8082284	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9635762	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9635763	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9891111	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9905583	0.92[EUR][1000 genomes]
rs9905922	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9911944	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv516872	chr17:45419139-45702280	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	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
4	nsv469573	chr17:45511582-45698942	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv471701	chr17:45511583-45698942	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	nsv471403	chr17:45608444-45700642	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv482203	chr17:45608444-45700642	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4793978	VPS25	cis	cerebellum	SCAN
rs4793978	VPS25	cis	parietal	SCAN
rs4793978	C17orf57	cis	cerebellum	SCAN
rs4793978	CDK5RAP3	cis	cerebellum	SCAN
rs4793978	NPEPPS	cis	parietal	SCAN
rs4793978	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs4793978	C17orf57	cis	parietal	SCAN
rs4793978	MRPL45P2	cis	lymphoblastoid	seeQTL
rs4793978	SLC25A39	cis	parietal	SCAN
rs4793978	DBF4B	cis	cerebellum	SCAN
rs4793978	TBKBP1	cis	Artery Tibial	GTEx
rs4793978	TBKBP1	cis	lymphoblastoid	seeQTL
rs4793978	TBKBP1	cis	Nerve Tibial	GTEx
rs4793978	RAB5C	cis	parietal	SCAN
rs4793978	C17orf65	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45659200-45698800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:45663800-45702800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr17:45665600-45698200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr17:45667200-45698600	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr17:45667400-45718200	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr17:45668200-45699000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr17:45670000-45703000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr17:45670200-45698600	Weak transcription	Fetal Heart	heart
9	chr17:45670400-45698200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr17:45672400-45704200	Strong transcription	Fetal Muscle Trunk	muscle
11	chr17:45672600-45703000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr17:45682200-45699000	Strong transcription	Fetal Muscle Leg	muscle
13	chr17:45682200-45699200	Weak transcription	Right Atrium	heart
14	chr17:45682800-45698800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr17:45682800-45702000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr17:45686800-45699400	Strong transcription	Fetal Intestine Small	intestine
17	chr17:45686800-45703400	Strong transcription	Fetal Stomach	stomach
18	chr17:45687600-45701400	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr17:45688000-45701600	Strong transcription	Primary T cells from cord blood	blood
20	chr17:45688600-45701400	Strong transcription	Dnd41	blood
21	chr17:45688800-45701600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr17:45688800-45702400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr17:45688800-45702400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr17:45688800-45703000	Strong transcription	Placenta	Placenta
25	chr17:45689000-45698400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr17:45689000-45703000	Strong transcription	Fetal Thymus	thymus
27	chr17:45689200-45698200	Weak transcription	Pancreas	Pancrea
28	chr17:45689200-45707800	Weak transcription	Gastric	stomach
29	chr17:45689400-45698800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr17:45689400-45698800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr17:45689400-45700400	Strong transcription	HepG2	liver
32	chr17:45689400-45701800	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr17:45689800-45698200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr17:45690400-45702000	Strong transcription	Fetal Intestine Large	intestine
35	chr17:45691600-45700200	Weak transcription	Esophagus	oesophagus
36	chr17:45691800-45698200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr17:45691800-45716600	Weak transcription	Right Ventricle	heart
38	chr17:45692800-45698800	Strong transcription	Colonic Mucosa	Colon
39	chr17:45692800-45714600	Weak transcription	Aorta	Aorta
40	chr17:45694000-45698600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr17:45694400-45699000	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr17:45694400-45701400	Strong transcription	Primary B cells from cord blood	blood
43	chr17:45694400-45701400	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr17:45694600-45698600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr17:45694600-45700600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr17:45694600-45702600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr17:45694600-45702600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr17:45694600-45702800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr17:45695000-45698800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr17:45695400-45698800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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