Variant report

Variant	rs4499701
Chromosome Location	chr4:106332199-106332200
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1017988	1.00[ASN][1000 genomes]
rs1077526	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1126066	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035461	0.85[EUR][1000 genomes]
rs17035550	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035551	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035553	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035557	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035558	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035568	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035581	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035584	1.00[ASN][1000 genomes]
rs17035586	1.00[ASN][1000 genomes]
rs17035619	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509136	1.00[ASN][1000 genomes]
rs2004290	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3898404	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519798	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55652556	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55755102	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55874621	1.00[ASN][1000 genomes]
rs56397029	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59902936	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62317353	1.00[ASN][1000 genomes]
rs6533194	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66517713	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66763438	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66932244	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66956902	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66988826	1.00[ASN][1000 genomes]
rs67248885	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67476913	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67554145	1.00[ASN][1000 genomes]
rs6811159	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829168	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856615	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857688	0.86[EUR][1000 genomes]
rs72668208	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668215	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668219	1.00[ASN][1000 genomes]
rs72668239	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4499701	PPA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106253800-106343000	Weak transcription	Psoas Muscle	Psoas
2	chr4:106279000-106339600	Weak transcription	HSMMtube	muscle
3	chr4:106279000-106347400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:106280000-106344600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr4:106282600-106335600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:106287000-106335800	Weak transcription	Colonic Mucosa	Colon
7	chr4:106287600-106335600	Weak transcription	Esophagus	oesophagus
8	chr4:106287600-106357000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:106287800-106335400	Weak transcription	Spleen	Spleen
10	chr4:106287800-106335800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:106287800-106347600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:106288600-106335400	Weak transcription	Thymus	Thymus
13	chr4:106289600-106335400	Weak transcription	Brain Anterior Caudate	brain
14	chr4:106290000-106347400	Weak transcription	Fetal Kidney	kidney
15	chr4:106290800-106345800	Weak transcription	K562	blood
16	chr4:106304400-106335600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:106306400-106335200	Weak transcription	Placenta	Placenta
18	chr4:106306400-106335400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:106306400-106335400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr4:106308400-106335800	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:106309400-106351000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:106312400-106335600	Weak transcription	Ovary	ovary
23	chr4:106314600-106335600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:106315600-106335400	Weak transcription	Pancreas	Pancrea
25	chr4:106317600-106336000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr4:106320800-106335600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr4:106320800-106335600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr4:106320800-106342800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:106320800-106342800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:106321000-106343600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr4:106321000-106346000	Weak transcription	Hela-S3	cervix
32	chr4:106321200-106335600	Weak transcription	Left Ventricle	heart
33	chr4:106321400-106367200	Weak transcription	HUVEC	blood vessel
34	chr4:106321600-106341800	Weak transcription	NH-A	brain
35	chr4:106321600-106356200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr4:106321800-106335600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:106321800-106353600	Weak transcription	HMEC	breast
38	chr4:106323600-106372800	Weak transcription	Stomach Mucosa	stomach
39	chr4:106324200-106347000	Weak transcription	Fetal Lung	lung
40	chr4:106326000-106335400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:106326000-106339800	Weak transcription	Brain Angular Gyrus	brain
42	chr4:106326000-106356400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr4:106326000-106356600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr4:106326000-106363200	Weak transcription	Colon Smooth Muscle	Colon
45	chr4:106326200-106335600	Weak transcription	Fetal Thymus	thymus
46	chr4:106326200-106347600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:106327200-106335400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:106327200-106335400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr4:106327200-106335400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:106327200-106335600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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