Variant report

Variant	rs818797
Chromosome Location	chr5:112219140-112219141
allele	C/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	HDAC2	chr5:112218957-112219186	K562	blood:	n/a	n/a
2	JUND	chr5:112219013-112219231	K562	blood:	n/a	n/a
3	GATA2	chr5:112218855-112219197	K562	blood:	n/a	n/a
4	EP300	chr5:112218900-112219206	K562	blood:	n/a	n/a
5	TAL1	chr5:112218930-112219183	K562	blood:	n/a	n/a
6	RCOR1	chr5:112218820-112219336	K562	blood:	n/a	n/a
7	BHLHE40	chr5:112219050-112219237	K562	blood:	n/a	n/a
8	RCOR1	chr5:112218866-112219274	K562	blood:	n/a	n/a
9	CEBPB	chr5:112218925-112219143	K562	blood:	n/a	n/a
10	POLR2A	chr5:112219034-112219314	MCF-7	breast:	n/a	n/a
11	NR2F2	chr5:112218917-112219222	K562	blood:	n/a	n/a
12	POLR2A	chr5:112219078-112219309	HepG2	liver:	n/a	n/a
13	ATF1	chr5:112218973-112219173	K562	blood:	n/a	n/a
14	TEAD4	chr5:112218794-112219310	K562	blood:	n/a	n/a
15	CEBPD	chr5:112218854-112219215	K562	blood:	n/a	n/a
16	POLR2A	chr5:112217858-112219262	K562	blood:	n/a	n/a

Variant related genes	Relation type
XBP1P1	TF binding region

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1093611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11241185	0.81[CEU][hapmap]
rs12518091	0.82[CEU][hapmap]
rs149130	0.85[CEU][hapmap]
rs149190	0.85[CEU][hapmap]
rs149191	0.82[EUR][1000 genomes]
rs149192	0.81[CEU][hapmap]
rs149193	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs153544	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs153546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs153548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs153549	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs153550	0.95[ASN][1000 genomes]
rs153551	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153552	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153556	0.85[EUR][1000 genomes]
rs153557	0.82[EUR][1000 genomes]
rs153561	0.82[EUR][1000 genomes]
rs153563	0.82[EUR][1000 genomes]
rs154344	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1974786	0.84[CEU][hapmap]
rs2431241	0.81[CEU][hapmap]
rs2431512	0.85[CEU][hapmap]
rs2545155	0.84[ASN][1000 genomes]
rs2545156	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2545170	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2546108	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs2546112	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs2546115	0.95[CHB][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs2707765	0.80[CHB][hapmap]
rs3317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs351767	0.92[ASN][1000 genomes]
rs351768	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs351770	1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs368575	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs373059	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs374613	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs382427	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs395858	0.96[CEU][hapmap];0.89[CHB][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs410701	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs414098	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs419155	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs448162	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs448613	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs454968	0.80[ASN][1000 genomes]
rs456531	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs459102	0.96[ASN][1000 genomes]
rs460137	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs467033	0.85[CEU][hapmap]
rs468610	0.83[ASN][1000 genomes]
rs468751	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs468854	0.88[ASN][1000 genomes]
rs469827	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs469886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4705486	0.81[CEU][hapmap]
rs4705559	0.85[CEU][hapmap]
rs4705608	0.82[CEU][hapmap]
rs4705610	0.85[CEU][hapmap]
rs4705624	0.80[CHB][hapmap]
rs495794	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs505382	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs514763	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs566419	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs6594646	0.85[CEU][hapmap]
rs67293732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712663	0.95[ASN][1000 genomes]
rs712670	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7213	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7704618	0.82[CEU][hapmap]
rs818426	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs818428	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs818429	0.96[ASN][1000 genomes]
rs818430	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs818782	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv870231	chr5:112192379-112247084	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1029595	chr5:112197662-112242375	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs818797	REEP5	cis	Esophagus Muscularis	GTEx
rs818797	REEP5	Cis_1M	lymphoblastoid	RTeQTL
rs818797	REEP5	cis	uninvolved skin	skin_eQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112198400-112220600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:112199000-112226000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:112200600-112242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:112206400-112242800	Weak transcription	Fetal Brain Male	brain
5	chr5:112206600-112219400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:112206600-112219800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr5:112206800-112220800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:112206800-112220800	Weak transcription	Ovary	ovary
9	chr5:112208200-112225800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:112209600-112225000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:112209600-112226400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr5:112209600-112226800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:112209800-112224600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:112209800-112238600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:112210600-112225000	Strong transcription	Liver	Liver
16	chr5:112210800-112225000	Strong transcription	Duodenum Mucosa	Duodenum
17	chr5:112210800-112232400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr5:112211200-112222600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:112211200-112240000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr5:112211600-112256400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:112211800-112223400	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr5:112211800-112239200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr5:112212200-112256400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr5:112212400-112220200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:112212400-112225200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:112212400-112225400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:112212600-112251400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr5:112213000-112223000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr5:112213000-112223200	Strong transcription	Fetal Lung	lung
30	chr5:112213000-112223200	Strong transcription	Stomach Smooth Muscle	stomach
31	chr5:112213000-112224600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:112213200-112222800	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr5:112213200-112223200	Strong transcription	Brain Germinal Matrix	brain
34	chr5:112213200-112223400	Strong transcription	Adipose Nuclei	Adipose
35	chr5:112213200-112223400	Strong transcription	Fetal Brain Female	brain
36	chr5:112213200-112229400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:112213600-112223000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr5:112213800-112219400	Strong transcription	Left Ventricle	heart
39	chr5:112213800-112225000	Strong transcription	Fetal Intestine Large	intestine
40	chr5:112214000-112223400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr5:112214000-112224400	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr5:112214200-112232200	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr5:112214800-112220800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:112214800-112220800	Weak transcription	Stomach Mucosa	stomach
45	chr5:112214800-112223400	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr5:112214800-112223400	Strong transcription	Fetal Thymus	thymus
47	chr5:112214800-112226600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:112214800-112234800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr5:112215000-112219600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr5:112215000-112220800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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