Variant report

Variant	rs17679445
Chromosome Location	chr17:46022065-46022066
allele	A/G
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	chr17:46020199-46023291	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:
2	chr17:46021116..46023804-chr17:46125669..46127456,2	K562	blood:
3	chr17:45978341..45980674-chr17:46019226..46022209,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234494	TF binding region
ENSG00000263798	TF binding region
PNPO	TF binding region
ENSG00000082641	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000167182	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10491182	1.00[CEU][hapmap]
rs10491183	1.00[CEU][hapmap]
rs11650043	1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11650304	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11651275	1.00[CEU][hapmap]
rs11651625	0.92[AMR][1000 genomes]
rs16949676	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17617360	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs17618704	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs41429650	1.00[CEU][hapmap]
rs4378657	0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7209072	1.00[CEU][hapmap]
rs7210041	1.00[CEU][hapmap]
rs9895554	1.00[CEU][hapmap]
rs9900074	1.00[CEU][hapmap]
rs9903963	1.00[CEU][hapmap]

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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	esv1000014	chr17:46019228-46029457	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17679445	PNPO	cis	Liver	GTEx
rs17679445	SKAP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019600-46027000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:46019800-46022200	Weak transcription	Right Ventricle	heart
3	chr17:46019800-46022600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr17:46019800-46022600	Weak transcription	Right Atrium	heart
5	chr17:46019800-46022800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr17:46019800-46022800	Weak transcription	Gastric	stomach
7	chr17:46019800-46022800	Weak transcription	Psoas Muscle	Psoas
8	chr17:46019800-46023400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr17:46019800-46024000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr17:46019800-46024800	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr17:46019800-46025600	Weak transcription	HSMM	muscle
12	chr17:46019800-46026800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr17:46019800-46026800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr17:46019800-46026800	Weak transcription	Brain Germinal Matrix	brain
15	chr17:46019800-46026800	Weak transcription	HSMMtube	muscle
16	chr17:46019800-46027400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr17:46019800-46034200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
19	chr17:46020000-46022200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr17:46020000-46022200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr17:46020000-46022200	Weak transcription	Brain Angular Gyrus	brain
22	chr17:46020000-46022200	Weak transcription	Brain Hippocampus Middle	brain
23	chr17:46020000-46022200	Weak transcription	Esophagus	oesophagus
24	chr17:46020000-46022200	Weak transcription	Fetal Brain Female	brain
25	chr17:46020000-46022200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr17:46020000-46022400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr17:46020000-46022600	Weak transcription	NHLF	lung
28	chr17:46020000-46022800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr17:46020000-46022800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr17:46020000-46024000	Weak transcription	Colon Smooth Muscle	Colon
31	chr17:46020000-46024400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr17:46020000-46026000	Weak transcription	Fetal Heart	heart
33	chr17:46020000-46026200	Weak transcription	Fetal Kidney	kidney
34	chr17:46020000-46026400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr17:46020000-46026400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr17:46020000-46026400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr17:46020000-46026800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr17:46020000-46026800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr17:46020000-46027000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr17:46020000-46034600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr17:46020200-46022200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr17:46020200-46022200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr17:46020200-46022200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr17:46020200-46022200	Weak transcription	A549	lung
45	chr17:46020200-46022400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr17:46020200-46022400	Weak transcription	Brain Substantia Nigra	brain
47	chr17:46020200-46022400	Weak transcription	NH-A	brain
48	chr17:46020200-46022600	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr17:46020200-46023000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr17:46020200-46026000	Weak transcription	NHDF-Ad	bronchial

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