Variant report

Variant	rs154344
Chromosome Location	chr5:112248738-112248739
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112196178..112198372-chr5:112245314..112249155,3	K562	blood:
2	chr5:112238334..112242783-chr5:112245993..112249269,4	K562	blood:
3	chr5:112246563..112249281-chr5:112250414..112253168,3	K562	blood:

Variant related genes	Relation type
ENSG00000272869	Chromatin interaction
ENSG00000153037	Chromatin interaction
ENSG00000266499	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1093611	0.85[ASN][1000 genomes]
rs149130	0.81[AMR][1000 genomes]
rs149190	0.82[EUR][1000 genomes]
rs149191	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs149193	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153544	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs153546	0.85[ASN][1000 genomes]
rs153548	0.85[ASN][1000 genomes]
rs153549	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs153550	0.85[ASN][1000 genomes]
rs153551	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs153552	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs153553	0.81[AMR][1000 genomes]
rs153556	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs153557	0.86[EUR][1000 genomes]
rs153561	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs153563	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs153565	0.81[AMR][1000 genomes]
rs2545156	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2545170	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2546115	0.82[ASN][1000 genomes]
rs3317	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs351767	0.85[ASN][1000 genomes]
rs351768	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs351770	0.83[ASN][1000 genomes]
rs368575	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs373059	0.84[EUR][1000 genomes]
rs374613	0.83[EUR][1000 genomes]
rs382427	0.83[EUR][1000 genomes]
rs395858	0.84[EUR][1000 genomes]
rs410701	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs419155	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs448613	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs456531	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs459102	0.85[ASN][1000 genomes]
rs460137	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs468610	0.89[ASN][1000 genomes]
rs468751	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs468854	0.94[ASN][1000 genomes]
rs469827	0.91[ASN][1000 genomes]
rs469886	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs495794	0.85[ASN][1000 genomes]
rs505382	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs514763	0.87[ASN][1000 genomes]
rs566419	0.81[AMR][1000 genomes]
rs67293732	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs712663	0.85[ASN][1000 genomes]
rs712670	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7213	0.85[ASN][1000 genomes]
rs818426	0.91[EUR][1000 genomes]
rs818428	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs818429	0.85[ASN][1000 genomes]
rs818430	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs818782	0.82[EUR][1000 genomes]
rs818797	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1030103	chr5:112197662-112255712	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv537863	chr5:112197662-112255712	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1019756	chr5:112242315-112325943	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs154344	REEP5	cis	Esophagus Muscularis	GTEx
rs154344	REEP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112211600-112256400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:112212200-112256400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:112212600-112251400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr5:112215200-112255800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:112221800-112256600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:112222000-112256400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:112223000-112256400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:112223000-112256600	Weak transcription	Thymus	Thymus
9	chr5:112224800-112250600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr5:112225000-112251600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:112229600-112250000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr5:112229600-112256600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr5:112230200-112251600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr5:112232600-112250200	Weak transcription	Stomach Mucosa	stomach
15	chr5:112234200-112249400	Weak transcription	Fetal Heart	heart
16	chr5:112237200-112249400	Weak transcription	K562	blood
17	chr5:112237400-112254000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:112238200-112249600	Weak transcription	Brain Germinal Matrix	brain
19	chr5:112238200-112251600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr5:112238400-112251800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:112238400-112252800	Weak transcription	Small Intestine	intestine
22	chr5:112238400-112253800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:112239000-112249200	Weak transcription	Hela-S3	cervix
24	chr5:112241200-112250400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:112241400-112249200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr5:112241800-112248800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr5:112242200-112254200	Weak transcription	Fetal Kidney	kidney
28	chr5:112242400-112250200	Strong transcription	HSMM	muscle
29	chr5:112242400-112252800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr5:112242600-112256800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr5:112243000-112249600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:112243200-112248800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr5:112243200-112249600	Weak transcription	Right Atrium	heart
34	chr5:112243200-112249800	Weak transcription	Spleen	Spleen
35	chr5:112243200-112251400	Weak transcription	Brain Angular Gyrus	brain
36	chr5:112243200-112254000	Weak transcription	Fetal Brain Male	brain
37	chr5:112243400-112249800	Weak transcription	Lung	lung
38	chr5:112243400-112250200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr5:112243400-112252800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr5:112244400-112249400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr5:112244600-112251600	Strong transcription	Primary B cells from peripheral blood	blood
42	chr5:112245800-112249400	Weak transcription	Right Ventricle	heart
43	chr5:112245800-112250200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr5:112245800-112252000	Weak transcription	Fetal Brain Female	brain
45	chr5:112245800-112252400	Weak transcription	Fetal Thymus	thymus
46	chr5:112245800-112252800	Weak transcription	Colonic Mucosa	Colon
47	chr5:112245800-112253200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr5:112245800-112253200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr5:112246000-112249600	Weak transcription	Fetal Stomach	stomach
50	chr5:112246000-112251400	Weak transcription	Fetal Lung	lung

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