Variant report

Variant	rs924283
Chromosome Location	chr4:106282165-106282166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPA2-5	chr4:106281485-106282259	NONHSAT097673

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10020998	0.87[CHB][hapmap]
rs1125254	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs11301777	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1603706	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17035512	0.82[AFR][1000 genomes]
rs2023840	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2046880	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2264415	0.97[ASN][1000 genomes]
rs2264416	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2264853	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2298732	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs2636693	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2636694	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2636695	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2636727	0.88[ASN][1000 genomes]
rs2636747	0.84[ASN][1000 genomes]
rs2647242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2647252	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2647255	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647265	0.93[ASN][1000 genomes]
rs2713826	1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2713844	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2713845	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2726456	0.98[ASN][1000 genomes]
rs2726496	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28561818	0.82[AFR][1000 genomes]
rs2866883	0.87[CHB][hapmap]
rs34248474	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs35206705	0.96[ASN][1000 genomes]
rs36112402	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3864225	0.87[CHB][hapmap]
rs41438151	1.00[ASW][hapmap];0.94[YRI][hapmap]
rs4698938	0.82[AFR][1000 genomes]
rs4699170	0.82[AFR][1000 genomes]
rs4699176	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs59939789	0.82[AFR][1000 genomes]
rs6533199	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs6533201	0.95[CHB][hapmap]
rs66712969	0.82[AFR][1000 genomes]
rs67209101	0.82[AFR][1000 genomes]
rs6816997	0.87[CHB][hapmap]
rs72665979	0.82[AFR][1000 genomes]
rs72665980	0.82[AFR][1000 genomes]
rs72665982	0.81[ASN][1000 genomes]
rs763289	0.87[CHB][hapmap]
rs7678401	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs7678439	0.94[YRI][hapmap]
rs924282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999896	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv879698	chr4:106155751-106309224	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS 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	41 gene(s)	inside rSNPs	diseases
6	nsv830027	chr4:106222010-106406738	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs924283	PPA2	cis	lymphoblastoid	seeQTL
rs924283	TET2	cis	parietal	SCAN
rs924283	PPA2	cis	multi-tissue	Pritchard
rs924283	PPA2	cis	Lymphoblastoid	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106252000-106287400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr4:106253800-106343000	Weak transcription	Psoas Muscle	Psoas
3	chr4:106265600-106282200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:106267000-106287200	Weak transcription	Liver	Liver
5	chr4:106268600-106287200	Weak transcription	Primary B cells from cord blood	blood
6	chr4:106272200-106286000	Weak transcription	Fetal Intestine Large	intestine
7	chr4:106272600-106291600	Weak transcription	Fetal Brain Male	brain
8	chr4:106272800-106304000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:106273400-106288200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:106273400-106293000	Weak transcription	Pancreas	Pancrea
11	chr4:106274200-106288200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:106274400-106326800	Weak transcription	Small Intestine	intestine
13	chr4:106274600-106283200	Weak transcription	Left Ventricle	heart
14	chr4:106274600-106287000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:106274600-106287000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:106274800-106294400	Weak transcription	HSMM	muscle
17	chr4:106274800-106330400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:106275200-106284200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr4:106275600-106287000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr4:106275800-106307800	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:106276800-106287000	Weak transcription	Spleen	Spleen
22	chr4:106277600-106288200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:106278200-106287000	Weak transcription	Fetal Stomach	stomach
24	chr4:106278400-106285600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:106278600-106287000	Weak transcription	Primary T cells from cord blood	blood
26	chr4:106278600-106307600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr4:106278800-106282200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr4:106278800-106282200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr4:106279000-106286600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:106279000-106339600	Weak transcription	HSMMtube	muscle
31	chr4:106279000-106347400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:106279200-106285600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:106279200-106287000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr4:106279200-106287400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:106279400-106287000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:106279400-106287000	Weak transcription	Brain Anterior Caudate	brain
37	chr4:106279600-106285600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:106279600-106287200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr4:106279600-106288600	Weak transcription	Fetal Kidney	kidney
40	chr4:106279800-106287200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:106279800-106288400	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr4:106280000-106283200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:106280000-106344600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr4:106280600-106285600	Weak transcription	Fetal Intestine Small	intestine
45	chr4:106280600-106290600	Weak transcription	Stomach Mucosa	stomach
46	chr4:106280800-106282200	Weak transcription	Fetal Muscle Leg	muscle
47	chr4:106280800-106283400	Weak transcription	Lung	lung
48	chr4:106280800-106285600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr4:106280800-106285600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:106280800-106285600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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