Variant report

Variant	rs16961516
Chromosome Location	chr17:17208232-17208233
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17138230..17139977-chr17:17206965..17208705,2	K562	blood:
2	chr17:17183059..17186537-chr17:17204352..17209458,5	K562	blood:
3	chr17:17135445..17137036-chr17:17206485..17208759,2	K562	blood:
4	chr17:17179045..17181973-chr17:17206782..17208341,2	MCF-7	breast:
5	chr17:17182421..17186483-chr17:17204152..17209830,5	MCF-7	breast:
6	chr17:17207386..17210121-chr17:17225925..17228746,2	K562	blood:
7	chr17:17207055..17208999-chr17:17214902..17216506,2	MCF-7	breast:
8	chr17:17109423..17111075-chr17:17206335..17209184,2	K562	blood:
9	chr17:17183415..17186229-chr17:17206165..17209020,3	MCF-7	breast:
10	chr17:17138440..17139977-chr17:17207205..17209555,2	K562	blood:
11	chr17:17181690..17186423-chr17:17204352..17210529,13	K562	blood:
12	chr17:17187827..17189746-chr17:17208127..17210298,2	MCF-7	breast:
13	chr17:17207665..17210654-chr17:17223210..17225727,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000266498	Chromatin interaction
ENSG00000179598	Chromatin interaction
ENSG00000154803	Chromatin interaction
ENSG00000141030	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs55708107	0.85[EUR][1000 genomes]
rs7211243	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7219752	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7226045	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv833380	chr17:17088416-17241206	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1065811	chr17:17104760-17225204	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv833382	chr17:17124329-17305683	Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv469777	chr17:17127385-17272698	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv482546	chr17:17127385-17272698	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1061186	chr17:17200427-17314406	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
7	esv3408202	chr17:17205752-17208600	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16961516	PIP4K2B	trans	brain	seeQTL
rs16961516	NT5M	cis	lymphoblastoid	seeQTL
rs16961516	NT5M	cis	multi-tissue	Pritchard

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17206000-17208600	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr17:17206200-17209400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:17207000-17209600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr17:17207000-17210000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr17:17207200-17208400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr17:17207200-17208400	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr17:17207200-17209000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
8	chr17:17207200-17209200	Flanking Active TSS	Dnd41	blood
9	chr17:17207200-17210200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr17:17207400-17208600	Enhancers	Brain Substantia Nigra	brain
11	chr17:17207400-17208600	Enhancers	Colonic Mucosa	Colon
12	chr17:17207400-17208600	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr17:17207400-17208800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr17:17207400-17208800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr17:17207400-17208800	Enhancers	Placenta	Placenta
16	chr17:17207400-17208800	Enhancers	Right Ventricle	heart
17	chr17:17207400-17209000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
18	chr17:17207400-17209200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr17:17207400-17209200	Flanking Active TSS	GM12878-XiMat	blood
20	chr17:17207400-17209400	Enhancers	Primary B cells from cord blood	blood
21	chr17:17207400-17209400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr17:17207400-17209600	Enhancers	Primary B cells from peripheral blood	blood
23	chr17:17207400-17209800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr17:17207400-17210200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr17:17207400-17215000	Weak transcription	Ovary	ovary
26	chr17:17207400-17235400	Weak transcription	Lung	lung
27	chr17:17207600-17208400	Bivalent Enhancer	Stomach Mucosa	stomach
28	chr17:17207600-17208400	Weak transcription	HSMM	muscle
29	chr17:17207600-17209000	Enhancers	HSMMtube	muscle
30	chr17:17207600-17209200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr17:17207600-17209400	Enhancers	Fetal Muscle Leg	muscle
32	chr17:17207600-17209600	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr17:17207600-17210000	Enhancers	HepG2	liver
34	chr17:17207600-17217800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr17:17207600-17246400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr17:17207800-17208400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
37	chr17:17207800-17208800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr17:17207800-17208800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr17:17207800-17208800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr17:17207800-17208800	Weak transcription	Fetal Intestine Small	intestine
41	chr17:17207800-17208800	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr17:17207800-17208800	Weak transcription	Osteobl	bone
43	chr17:17207800-17209200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr17:17207800-17209200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr17:17207800-17209200	Enhancers	Fetal Brain Male	brain
46	chr17:17207800-17209200	Enhancers	Fetal Brain Female	brain
47	chr17:17207800-17209200	Enhancers	Fetal Muscle Trunk	muscle
48	chr17:17207800-17209800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr17:17207800-17211200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr17:17207800-17212800	Enhancers	Primary monocytes fromperipheralblood	blood

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