Variant report

Variant	rs59902936
Chromosome Location	chr4:106317069-106317070
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1017988	1.00[ASN][1000 genomes]
rs1077526	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1126066	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035461	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17035475	0.81[AMR][1000 genomes]
rs17035478	0.81[AMR][1000 genomes]
rs17035550	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035551	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035553	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035557	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035558	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035568	0.82[AFR][1000 genomes];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	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28561818	0.81[AMR][1000 genomes]
rs34628486	0.81[AMR][1000 genomes]
rs3898404	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41438151	0.81[AMR][1000 genomes]
rs4499701	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519798	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698937	0.81[AMR][1000 genomes]
rs4699169	0.81[AMR][1000 genomes]
rs4699172	0.81[AMR][1000 genomes]
rs55652556	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55755102	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55758341	0.81[AMR][1000 genomes]
rs55874621	1.00[ASN][1000 genomes]
rs56184249	0.81[AMR][1000 genomes]
rs56387770	0.81[AMR][1000 genomes]
rs56397029	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58566149	0.81[AMR][1000 genomes]
rs59738222	0.81[AMR][1000 genomes]
rs59939789	0.81[AMR][1000 genomes]
rs62317353	1.00[ASN][1000 genomes]
rs6533188	0.81[AMR][1000 genomes]
rs6533194	0.93[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	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66867451	0.81[AMR][1000 genomes]
rs66932244	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66956902	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66988826	1.00[ASN][1000 genomes]
rs67075366	0.81[AMR][1000 genomes]
rs67104841	0.81[AMR][1000 genomes]
rs67124324	0.81[AMR][1000 genomes]
rs67248885	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67457538	0.81[AMR][1000 genomes]
rs67476913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67554145	1.00[ASN][1000 genomes]
rs6811159	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68146425	0.81[AMR][1000 genomes]
rs6829168	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856615	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857688	0.86[EUR][1000 genomes]
rs72665984	0.81[AMR][1000 genomes]
rs72668208	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668219	1.00[ASN][1000 genomes]
rs72668239	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656023	0.81[AMR][1000 genomes]
rs7673307	0.81[AMR][1000 genomes]
rs7678439	0.81[AMR][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
rs59902936	PPA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 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	chr4:106274400-106326800	Weak transcription	Small Intestine	intestine
3	chr4:106274800-106330400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:106279000-106339600	Weak transcription	HSMMtube	muscle
5	chr4:106279000-106347400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:106280000-106344600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr4:106281000-106326800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:106282600-106325800	Weak transcription	Brain Angular Gyrus	brain
9	chr4:106282600-106335600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr4:106283600-106330000	Weak transcription	Right Ventricle	heart
11	chr4:106285000-106326000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:106287000-106320800	Weak transcription	NH-A	brain
13	chr4:106287000-106335800	Weak transcription	Colonic Mucosa	Colon
14	chr4:106287600-106335600	Weak transcription	Esophagus	oesophagus
15	chr4:106287600-106357000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:106287800-106318600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:106287800-106320000	Weak transcription	A549	lung
18	chr4:106287800-106326800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:106287800-106330200	Weak transcription	Gastric	stomach
20	chr4:106287800-106335400	Weak transcription	Spleen	Spleen
21	chr4:106287800-106335800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:106287800-106347600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:106288400-106318600	Weak transcription	Aorta	Aorta
24	chr4:106288400-106330200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:106288400-106330200	Weak transcription	Lung	lung
26	chr4:106288600-106325600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:106288600-106335400	Weak transcription	Thymus	Thymus
28	chr4:106288800-106320600	Weak transcription	NHEK	skin
29	chr4:106288800-106325600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr4:106289200-106325600	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:106289600-106335400	Weak transcription	Brain Anterior Caudate	brain
32	chr4:106290000-106347400	Weak transcription	Fetal Kidney	kidney
33	chr4:106290800-106325600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:106290800-106345800	Weak transcription	K562	blood
35	chr4:106291200-106319800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:106291200-106320600	Weak transcription	NHLF	lung
37	chr4:106293400-106330200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:106294800-106320600	Weak transcription	HSMM	muscle
39	chr4:106297000-106320400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr4:106298000-106320600	Weak transcription	HMEC	breast
41	chr4:106301200-106320400	Weak transcription	Hela-S3	cervix
42	chr4:106304200-106326800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:106304400-106330400	Weak transcription	Fetal Stomach	stomach
44	chr4:106304400-106335600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:106305000-106325800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:106305400-106325800	Weak transcription	Fetal Intestine Small	intestine
47	chr4:106306400-106317200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr4:106306400-106318800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr4:106306400-106325600	Weak transcription	Colon Smooth Muscle	Colon
50	chr4:106306400-106325800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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