Variant report

Variant	rs55915354
Chromosome Location	chr4:57370023-57370024
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr4:57369971-57370239	K562	blood:	n/a	chr4:57370106-57370117
2	CEBPB	chr4:57370011-57370272	HepG2	liver:	n/a	chr4:57370106-57370117
3	POLR2A	chr4:57369753-57370182	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ARL9	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10013402	0.80[ASN][1000 genomes]
rs10051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434444	0.81[ASN][1000 genomes]
rs1060472	0.81[ASN][1000 genomes]
rs11133442	0.87[ASN][1000 genomes]
rs12501334	0.81[ASN][1000 genomes]
rs12503412	0.81[ASN][1000 genomes]
rs12505767	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12505939	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508008	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12509542	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12510712	0.83[ASN][1000 genomes]
rs12511770	0.89[ASN][1000 genomes]
rs12513091	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12646890	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs14211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474179	0.90[ASN][1000 genomes]
rs17086696	0.80[ASN][1000 genomes]
rs17086794	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17086832	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17086853	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1967559	0.87[ASN][1000 genomes]
rs1983378	0.81[ASN][1000 genomes]
rs2030366	0.81[ASN][1000 genomes]
rs28866881	0.81[ASN][1000 genomes]
rs4340842	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4346704	0.89[ASN][1000 genomes]
rs4618376	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864579	0.80[ASN][1000 genomes]
rs4864580	0.80[ASN][1000 genomes]
rs4864583	0.81[ASN][1000 genomes]
rs4864585	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4865092	0.82[ASN][1000 genomes]
rs4865103	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4865107	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4865108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56040009	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56099714	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56229630	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56392224	0.81[ASN][1000 genomes]
rs56887793	0.82[ASN][1000 genomes]
rs58151706	0.80[ASN][1000 genomes]
rs58333131	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6554358	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66858948	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66863699	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6820314	0.81[ASN][1000 genomes]
rs6821301	0.92[ASN][1000 genomes]
rs6824893	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6829250	0.81[ASN][1000 genomes]
rs6834696	0.83[ASN][1000 genomes]
rs6849183	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7664841	0.92[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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv829941	chr4:57359551-57553136	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs55915354	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs55915354	SRP72	cis	Whole Blood	GTEx
rs55915354	SRP72	Cis_1M	lymphoblastoid	RTeQTL
rs55915354	SRP72	cis	Esophagus Mucosa	GTEx
rs55915354	SRP72	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57334800-57371200	Weak transcription	Stomach Mucosa	stomach
2	chr4:57335200-57371400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:57335600-57370200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr4:57335800-57370200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr4:57335800-57370800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:57336000-57370200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:57336000-57371000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:57336200-57370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:57336400-57370200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:57342000-57370200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr4:57342400-57370800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr4:57342400-57371400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:57346000-57371400	Weak transcription	Pancreas	Pancrea
14	chr4:57352000-57371400	Weak transcription	Gastric	stomach
15	chr4:57352000-57371400	Weak transcription	Spleen	Spleen
16	chr4:57353800-57371400	Weak transcription	Fetal Brain Male	brain
17	chr4:57354600-57371400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr4:57356600-57371400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:57357400-57371400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr4:57357400-57371800	Weak transcription	Small Intestine	intestine
21	chr4:57357600-57371400	Weak transcription	Brain Substantia Nigra	brain
22	chr4:57357800-57371200	Weak transcription	Colonic Mucosa	Colon
23	chr4:57359200-57371200	Weak transcription	Hela-S3	cervix
24	chr4:57360400-57371200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:57361200-57371400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:57362400-57371400	Weak transcription	Aorta	Aorta
27	chr4:57362400-57371400	Weak transcription	Esophagus	oesophagus
28	chr4:57362400-57371400	Weak transcription	Right Ventricle	heart
29	chr4:57362600-57371400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:57362600-57371400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:57362800-57371400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr4:57363000-57371400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:57363000-57371400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr4:57363200-57371200	Weak transcription	Fetal Stomach	stomach
35	chr4:57363200-57371400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr4:57363200-57371400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:57363200-57371400	Weak transcription	Fetal Lung	lung
38	chr4:57363200-57371400	Weak transcription	Ovary	ovary
39	chr4:57363200-57371400	Weak transcription	NHLF	lung
40	chr4:57363200-57371600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:57363200-57371600	Weak transcription	Lung	lung
42	chr4:57363800-57371400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr4:57363800-57371600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:57364000-57371200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:57364000-57371400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:57364000-57371400	Weak transcription	Brain Angular Gyrus	brain
47	chr4:57364200-57371400	Weak transcription	Brain Germinal Matrix	brain
48	chr4:57365800-57370200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr4:57365800-57370200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr4:57366000-57370200	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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