Variant report

Variant	rs1713495
Chromosome Location	chr17:45200472-45200473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45195494..45197087-chr17:45199093..45201965,2	K562	blood:

Variant related genes	Relation type
ENSG00000221016	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1515751	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap]
rs1515752	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap]
rs1634268	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1713494	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs188799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2071438	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap]
rs221597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs221598	1.00[CEU][hapmap]
rs221599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs221602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2678694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3785875	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4968309	0.92[ASW][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs6504745	0.95[ASN][1000 genomes]
rs701982	0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs764792	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs8071382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8076808	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs858679	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs938904	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897015	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9905948	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	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
3	nsv833467	chr17:45063935-45252624	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3332795	chr17:45116212-45209297	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	13 gene(s)	inside rSNPs	diseases
5	esv3386521	chr17:45116232-45209267	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1059766	chr17:45130765-45203468	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	esv2760450	chr17:45130777-45225222	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv908563	chr17:45158537-45230311	ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv962456	chr17:45163689-45212872	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1713495	DBF4B	cis	parietal	SCAN
rs1713495	ACLY	cis	parietal	SCAN
rs1713495	NMT1	cis	cerebellum	SCAN
rs1713495	SOST	cis	cerebellum	SCAN
rs1713495	TOP2A	cis	cerebellum	SCAN
rs1713495	MYL4	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45185600-45206400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr17:45190000-45203200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr17:45191000-45202000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr17:45191200-45202600	Weak transcription	Right Ventricle	heart
5	chr17:45192400-45212800	Weak transcription	Gastric	stomach
6	chr17:45193200-45212800	Weak transcription	Aorta	Aorta
7	chr17:45194000-45209800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr17:45194200-45204600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr17:45194200-45208200	Strong transcription	HUVEC	blood vessel
10	chr17:45194200-45209600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr17:45194200-45209600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr17:45194200-45209800	Strong transcription	Dnd41	blood
13	chr17:45194400-45201000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr17:45194800-45203600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr17:45194800-45212800	Weak transcription	Colonic Mucosa	Colon
16	chr17:45194800-45214400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr17:45194800-45234200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr17:45195400-45201200	Strong transcription	Liver	Liver
19	chr17:45195400-45209600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr17:45195400-45209800	Strong transcription	Fetal Thymus	thymus
21	chr17:45195600-45203200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr17:45195600-45209400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr17:45195800-45201600	Strong transcription	Adipose Nuclei	Adipose
24	chr17:45195800-45212800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr17:45196000-45201400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr17:45196000-45205600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr17:45196000-45206400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr17:45196000-45209600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:45196000-45209800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr17:45196200-45212800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:45196400-45204200	Weak transcription	Lung	lung
32	chr17:45196400-45204200	Weak transcription	Spleen	Spleen
33	chr17:45196400-45212800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr17:45196400-45212800	Weak transcription	Ovary	ovary
35	chr17:45196600-45207400	Strong transcription	Placenta	Placenta
36	chr17:45196600-45213000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:45196600-45213000	Weak transcription	Esophagus	oesophagus
38	chr17:45197000-45207000	Strong transcription	Fetal Lung	lung
39	chr17:45197200-45201400	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr17:45197200-45201600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr17:45197200-45206800	Strong transcription	GM12878-XiMat	blood
42	chr17:45197200-45207400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr17:45197200-45209600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr17:45197400-45201400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr17:45197400-45206400	Strong transcription	Brain Germinal Matrix	brain
46	chr17:45197400-45206800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr17:45197400-45209800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr17:45197600-45201600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr17:45197600-45201600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr17:45197600-45202200	Strong transcription	HepG2	liver

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