Variant report

Variant	rs2288489
Chromosome Location	chr16:71509685-71509686
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71508819..71510748-chr16:71511995..71514492,2	K562	blood:
2	chr16:71504762..71507236-chr16:71509593..71512439,2	K562	blood:
3	chr16:71508758..71510611-chr16:71516213..71518587,2	MCF-7	breast:
4	chr16:71507450..71511299-chr16:71511883..71513820,5	K562	blood:
5	chr16:71494025..71497980-chr16:71506815..71510228,4	K562	blood:
6	chr16:71508246..71511064-chr16:71516547..71519494,2	K562	blood:

Variant related genes	Relation type
ENSG00000247324	Chromatin interaction
ENSG00000167377	Chromatin interaction
ENSG00000157429	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12446461	0.91[YRI][hapmap]
rs310334	0.85[LWK][hapmap];0.91[YRI][hapmap]
rs3813743	0.86[LWK][hapmap]
rs4149497	0.82[GIH][hapmap];0.95[MEX][hapmap]
rs732318	0.91[YRI][hapmap]
rs8050871	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs8051212	0.89[LWK][hapmap];0.91[YRI][hapmap]
rs8061078	1.00[YRI][hapmap]
rs9936249	0.81[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv3411957	chr16:71509290-71510579	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2288489	PHLPP2	cis	lymphoblastoid	seeQTL
rs2288489	LRRC29	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71496600-71511400	Weak transcription	Pancreas	Pancrea
2	chr16:71496800-71512000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr16:71496800-71512200	Weak transcription	Fetal Intestine Small	intestine
4	chr16:71497000-71511800	Weak transcription	Brain Substantia Nigra	brain
5	chr16:71497000-71517400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr16:71497000-71517400	Weak transcription	Fetal Heart	heart
7	chr16:71497000-71517600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr16:71497400-71509800	Weak transcription	Spleen	Spleen
9	chr16:71502800-71517400	Weak transcription	Dnd41	blood
10	chr16:71504400-71509800	Weak transcription	Fetal Kidney	kidney
11	chr16:71504400-71512800	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr16:71504600-71513600	Strong transcription	Stomach Smooth Muscle	stomach
13	chr16:71504800-71512800	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr16:71504800-71513000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr16:71505000-71513000	Strong transcription	Adipose Nuclei	Adipose
16	chr16:71505600-71509800	Weak transcription	GM12878-XiMat	blood
17	chr16:71505800-71509800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr16:71506400-71517400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr16:71507200-71510000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr16:71507200-71514800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr16:71507200-71517800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr16:71507400-71517800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr16:71507600-71512800	Strong transcription	Ovary	ovary
24	chr16:71507600-71513000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr16:71507600-71517400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr16:71507600-71517400	Weak transcription	Fetal Brain Male	brain
27	chr16:71507800-71512600	Strong transcription	Fetal Brain Female	brain
28	chr16:71507800-71512800	Strong transcription	Left Ventricle	heart
29	chr16:71507800-71513000	Strong transcription	Aorta	Aorta
30	chr16:71507800-71513000	Strong transcription	Brain Germinal Matrix	brain
31	chr16:71507800-71513000	Strong transcription	Fetal Muscle Leg	muscle
32	chr16:71507800-71513200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr16:71508000-71513000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr16:71508200-71510200	Strong transcription	Primary hematopoietic stem cells	blood
35	chr16:71508200-71513000	Strong transcription	Liver	Liver
36	chr16:71508400-71511600	Weak transcription	Fetal Stomach	stomach
37	chr16:71508400-71511800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr16:71508400-71512200	Strong transcription	Placenta	Placenta
39	chr16:71508400-71512400	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr16:71508400-71512600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr16:71508400-71512800	Strong transcription	Brain Anterior Caudate	brain
42	chr16:71508400-71513000	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr16:71508400-71517600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr16:71508400-71517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr16:71508600-71511800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr16:71508600-71511800	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr16:71508600-71512800	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr16:71508600-71512800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr16:71508600-71512800	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr16:71508600-71513000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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