Variant report

Variant	rs153557
Chromosome Location	chr5:112257366-112257367
allele	A/C/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	HA-E2F1	chr5:112256585-112258414	MCF-7	breast:	n/a	chr5:112257583-112257593 chr5:112257346-112257356 chr5:112257539-112257549 chr5:112258101-112258110
2	MAZ	chr5:112256683-112258294	HepG2	liver:	n/a	chr5:112257350-112257360 chr5:112258184-112258193 chr5:112257755-112257765
3	POLR2A	chr5:112256715-112260053	GM12878	blood:	n/a	n/a
4	YY1	chr5:112257006-112258241	HepG2	liver:	n/a	chr5:112258098-112258107 chr5:112257579-112257590 chr5:112257715-112257726 chr5:112257582-112257596 chr5:112257532-112257546 chr5:112257960-112257971 chr5:112257717-112257731
5	POLR2A	chr5:112256673-112259684	GM19099	blood:	n/a	n/a
6	POLR2A	chr5:112256731-112257553	HL-60	blood:	n/a	n/a
7	MAX	chr5:112257190-112257454	HepG2	liver:	n/a	chr5:112257350-112257360
8	YY1	chr5:112257033-112257473	K562	blood:	n/a	n/a
9	CTCF	chr5:112257260-112257410	HPAF	blood vessel:	n/a	chr5:112257368-112257381
10	ELF1	chr5:112256688-112258324	GM12878	blood:	n/a	chr5:112257537-112257549 chr5:112257240-112257253 chr5:112258099-112258111 chr5:112257241-112257250
11	POLR2A	chr5:112256482-112258299	GM12878	blood:	n/a	n/a
12	CTCF	chr5:112257300-112257450	GM12866	blood:	n/a	chr5:112257368-112257381
13	POLR2A	chr5:112257065-112257644	A549	lung:	n/a	n/a
14	TBL1XR1	chr5:112256782-112258272	GM12878	blood:	n/a	n/a
15	STAT5A	chr5:112256933-112257395	GM12878	blood:	n/a	n/a
16	RCOR1	chr5:112256646-112257539	K562	blood:	n/a	n/a
17	MAX	chr5:112256708-112258301	A549	lung:	n/a	chr5:112257350-112257360 chr5:112258184-112258193 chr5:112257755-112257765
18	HEY1	chr5:112256654-112258161	HepG2	liver:	n/a	chr5:112257551-112257566 chr5:112257529-112257544 chr5:112257940-112257955 chr5:112257967-112257982 chr5:112257270-112257285
19	MAX	chr5:112256655-112258338	K562	blood:	n/a	chr5:112257350-112257360 chr5:112258184-112258193 chr5:112257755-112257765
20	YY1	chr5:112256798-112257555	GM12892	blood:	n/a	chr5:112257532-112257546
21	MYC	chr5:112256686-112257516	MCF10A-Er-Src	breast:	n/a	chr5:112257350-112257360
22	POLR2A	chr5:112256787-112258337	GM19193	blood:	n/a	n/a
23	CTCF	chr5:112257240-112257390	K562	blood:	n/a	chr5:112257368-112257381
24	POLR2A	chr5:112256792-112258103	K562	blood:	n/a	n/a
25	CTCF	chr5:112257240-112257390	HCPEpiC	choroid plexus:	n/a	chr5:112257368-112257381
26	TBL1XR1	chr5:112257076-112257479	K562	blood:	n/a	n/a
27	MXI1	chr5:112256743-112258274	HepG2	liver:	n/a	n/a
28	POLR2A	chr5:112256522-112257615	U87	brain:	n/a	n/a
29	POLR2A	chr5:112256537-112258020	K562	blood:	n/a	n/a
30	HMGN3	chr5:112256914-112258322	K562	blood:	n/a	n/a
31	PML	chr5:112256724-112257487	K562	blood:	n/a	n/a
32	POLR2A	chr5:112256654-112258191	K562	blood:	n/a	n/a
33	POLR2A	chr5:112256663-112258295	MCF-7	breast:	n/a	n/a
34	CTCF	chr5:112257280-112257430	GM12864	blood:	n/a	chr5:112257368-112257381
35	YY1	chr5:112257063-112257651	GM12891	blood:	n/a	chr5:112257579-112257590 chr5:112257582-112257596 chr5:112257532-112257546
36	CTCF	chr5:112257296-112257434	A549	lung:	n/a	chr5:112257368-112257381
37	CTCF	chr5:112257278-112257442	HepG2	liver:	n/a	chr5:112257368-112257381
38	TCF7L2	chr5:112256839-112258259	HCT-116	colon:	n/a	n/a
39	POLR2A	chr5:112256780-112258325	Raji	blood:	n/a	n/a
40	UBTF	chr5:112256463-112258226	K562	blood:	n/a	n/a
41	HEY1	chr5:112256968-112258019	K562	blood:	n/a	chr5:112257551-112257566 chr5:112257529-112257544 chr5:112257940-112257955 chr5:112257967-112257982 chr5:112257270-112257285
42	MAX	chr5:112256603-112258348	ECC-1	luminal epithelium:	n/a	chr5:112257350-112257360 chr5:112258184-112258193 chr5:112257755-112257765
43	YY1	chr5:112256563-112258335	SK-N-SH	brain:	n/a	chr5:112258098-112258107 chr5:112257579-112257590 chr5:112257715-112257726 chr5:112257582-112257596 chr5:112257532-112257546 chr5:112257960-112257971 chr5:112257717-112257731
44	RCOR1	chr5:112256843-112257368	GM12878	blood:	n/a	n/a
45	CTCF	chr5:112257320-112257470	HAc	cerebellar:	n/a	chr5:112257368-112257381
46	CTCF	chr5:112257300-112257450	GM12871	blood:	n/a	chr5:112257368-112257381
47	CTCF	chr5:112257018-112257481	GM12878	blood:	n/a	chr5:112257368-112257381
48	CTCF	chr5:112257342-112257422	HepG2	liver:	n/a	chr5:112257368-112257381
49	POLR2A	chr5:112256605-112257550	HCT-116	colon:	n/a	n/a
50	POLR2A	chr5:112256672-112258241	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:112255914..112262078-chr5:112308752..112315375,16	MCF-7	breast:
2	chr14:102543693..102544490-chr5:112257112..112258011,2	HCT-116	colon:
3	chr5:112253961..112259306-chr5:112310933..112315767,8	K562	blood:
4	chr5:112196028..112199860-chr5:112256680..112260462,5	MCF-7	breast:
5	chr5:112255746..112257849-chr5:112312359..112314246,3	MCF-7	breast:
6	chr5:112223765..112227904-chr5:112256681..112259724,3	K562	blood:
7	chr5:112195239..112200315-chr5:112255126..112261929,8	MCF-7	breast:
8	chr16:81069322..81070029-chr5:112256640..112257405,2	Hela-S3	cervix:
9	chr5:111496112..111498947-chr5:112256676..112259616,2	K562	blood:
10	chr5:112255209..112259355-chr5:112310614..112316433,9	K562	blood:

Variant related genes	Relation type
REEP5	TF binding region
ENSG00000240457	Chromatin interaction
ENSG00000260213	Chromatin interaction
ENSG00000272869	Chromatin interaction
ENSG00000166454	Chromatin interaction
ENSG00000238363	Chromatin interaction
ENSG00000224032	Chromatin interaction
ENSG00000153037	Chromatin interaction
ENSG00000212643	Chromatin interaction
ENSG00000172795	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs149130	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs149190	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs149191	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs149192	0.82[EUR][1000 genomes]
rs149193	0.87[EUR][1000 genomes]
rs151979	0.93[ASN][1000 genomes]
rs151980	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs153544	0.86[EUR][1000 genomes]
rs153551	0.80[EUR][1000 genomes]
rs153553	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs153556	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs153559	0.83[EUR][1000 genomes]
rs153561	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs153563	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs153569	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs154344	0.86[EUR][1000 genomes]
rs1644099	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17135222	0.86[ASN][1000 genomes]
rs2545156	0.81[EUR][1000 genomes]
rs2545170	0.82[EUR][1000 genomes]
rs3317	0.84[EUR][1000 genomes]
rs351768	0.81[EUR][1000 genomes]
rs368575	0.84[EUR][1000 genomes]
rs410701	0.84[EUR][1000 genomes]
rs419155	0.84[EUR][1000 genomes]
rs448613	0.84[EUR][1000 genomes]
rs456531	0.84[EUR][1000 genomes]
rs467660	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs468751	0.84[EUR][1000 genomes]
rs469523	0.84[ASN][1000 genomes]
rs469675	0.84[ASN][1000 genomes]
rs469753	0.87[ASN][1000 genomes]
rs469886	0.84[EUR][1000 genomes]
rs67293732	0.82[EUR][1000 genomes]
rs712670	0.83[EUR][1000 genomes]
rs818426	0.82[EUR][1000 genomes]
rs818428	0.85[EUR][1000 genomes]
rs818430	0.85[EUR][1000 genomes]
rs818797	0.82[EUR][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	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
5	esv2763866	chr5:112254282-112284223	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3393782	chr5:112256103-112258601	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs153557	REEP5	Cis_1M	lymphoblastoid	RTeQTL
rs153557	REEP5	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112255400-112258400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:112255600-112258200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:112256000-112258200	Active TSS	NHDF-Ad	bronchial
4	chr5:112256200-112257400	Active TSS	Fetal Brain Female	brain
5	chr5:112256200-112258000	Active TSS	NHLF	lung
6	chr5:112256200-112258200	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr5:112256200-112258200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:112256200-112258200	Active TSS	GM12878-XiMat	blood
9	chr5:112256200-112258400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr5:112256200-112258600	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr5:112256400-112257400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr5:112256400-112257400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:112256400-112257400	Active TSS	Brain Germinal Matrix	brain
14	chr5:112256400-112257800	Active TSS	Right Atrium	heart
15	chr5:112256400-112258000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:112256400-112258000	Active TSS	Colonic Mucosa	Colon
17	chr5:112256400-112258200	Active TSS	H1 Cell Line	embryonic stem cell
18	chr5:112256400-112258200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr5:112256400-112258200	Active TSS	Placenta	Placenta
20	chr5:112256400-112258200	Active TSS	Gastric	stomach
21	chr5:112256400-112258200	Active TSS	Psoas Muscle	Psoas
22	chr5:112256400-112258200	Active TSS	HSMM	muscle
23	chr5:112256400-112258400	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr5:112256400-112258400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:112256400-112258400	Active TSS	H9 Cell Line	embryonic stem cell
26	chr5:112256400-112258400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:112256400-112258400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:112256400-112258400	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr5:112256400-112258400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:112256400-112258400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:112256400-112258400	Active TSS	Aorta	Aorta
32	chr5:112256400-112258400	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr5:112256400-112258400	Active TSS	Left Ventricle	heart
34	chr5:112256400-112258400	Active TSS	Ovary	ovary
35	chr5:112256400-112258400	Active TSS	Pancreas	Pancrea
36	chr5:112256400-112258400	Active TSS	Right Ventricle	heart
37	chr5:112256400-112258600	Active TSS	Fetal Muscle Trunk	muscle
38	chr5:112256600-112257800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr5:112256600-112258000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:112256600-112258000	Active TSS	Small Intestine	intestine
41	chr5:112256600-112258200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:112256600-112258200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr5:112256600-112258200	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr5:112256600-112258200	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr5:112256600-112258200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:112256600-112258200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:112256600-112258200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:112256600-112258200	Active TSS	Brain Hippocampus Middle	brain
49	chr5:112256600-112258200	Active TSS	Brain Substantia Nigra	brain
50	chr5:112256600-112258200	Active TSS	Fetal Intestine Large	intestine

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