Variant report

Variant	rs153556
Chromosome Location	chr5:112257908-112257909
allele	A/G
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	EP300	chr5:112257580-112258242	T-47D	breast:	n/a	chr5:112257963-112257979
3	POLR2A	chr5:112257634-112258035	GM12892	blood:	n/a	n/a
4	MAX	chr5:112257700-112258011	K562	blood:	n/a	chr5:112257755-112257765
5	POLR2A	chr5:112257653-112258117	GM12878	blood:	n/a	n/a
6	CTCF	chr5:112257732-112258300	K562	blood:	n/a	n/a
7	MAZ	chr5:112256683-112258294	HepG2	liver:	n/a	chr5:112257350-112257360 chr5:112258184-112258193 chr5:112257755-112257765
8	POLR2A	chr5:112256715-112260053	GM12878	blood:	n/a	n/a
9	ZNF143	chr5:112257774-112258282	K562	blood:	n/a	chr5:112258110-112258128
10	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
11	POLR2A	chr5:112256673-112259684	GM19099	blood:	n/a	n/a
12	YY1	chr5:112257693-112258292	H1-hESC	embryonic stem cell:	n/a	chr5:112258098-112258107 chr5:112257715-112257726 chr5:112257960-112257971 chr5:112257717-112257731
13	CTCF	chr5:112257883-112258266	Spleen_OC	spleen:	n/a	n/a
14	ARID3A	chr5:112257795-112258246	HepG2	liver:	n/a	n/a
15	ELF1	chr5:112256688-112258324	GM12878	blood:	n/a	chr5:112257537-112257549 chr5:112257240-112257253 chr5:112258099-112258111 chr5:112257241-112257250
16	REST	chr5:112257597-112258011	PFSK-1	brain:	n/a	chr5:112257910-112257930 chr5:112257705-112257725 chr5:112257709-112257722 chr5:112257712-112257725 chr5:112257706-112257724 chr5:112257705-112257725
17	POLR2A	chr5:112256482-112258299	GM12878	blood:	n/a	n/a
18	POLR2A	chr5:112257510-112258222	GM12892	blood:	n/a	n/a
19	TBL1XR1	chr5:112256782-112258272	GM12878	blood:	n/a	n/a
20	MAX	chr5:112256708-112258301	A549	lung:	n/a	chr5:112257350-112257360 chr5:112258184-112258193 chr5:112257755-112257765
21	HEY1	chr5:112256654-112258161	HepG2	liver:	n/a	chr5:112257551-112257566 chr5:112257529-112257544 chr5:112257940-112257955 chr5:112257967-112257982 chr5:112257270-112257285
22	MAX	chr5:112256655-112258338	K562	blood:	n/a	chr5:112257350-112257360 chr5:112258184-112258193 chr5:112257755-112257765
23	FOXP2	chr5:112257708-112258273	PFSK-1	brain:	n/a	n/a
24	ZMIZ1	chr5:112257679-112258246	K562	blood:	n/a	n/a
25	MXI1	chr5:112257566-112258258	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr5:112256787-112258337	GM19193	blood:	n/a	n/a
27	POLR2A	chr5:112256792-112258103	K562	blood:	n/a	n/a
28	JUND	chr5:112257677-112258241	A549	lung:	n/a	n/a
29	MXI1	chr5:112256743-112258274	HepG2	liver:	n/a	n/a
30	POLR2A	chr5:112256537-112258020	K562	blood:	n/a	n/a
31	HMGN3	chr5:112256914-112258322	K562	blood:	n/a	n/a
32	RUNX3	chr5:112257459-112258578	GM12878	blood:	n/a	n/a
33	POLR2A	chr5:112256654-112258191	K562	blood:	n/a	n/a
34	CTCF	chr5:112257864-112258302	H1-hESC	embryonic stem cell:	n/a	n/a
35	ZNF143	chr5:112257823-112258278	H1-hESC	embryonic stem cell:	n/a	chr5:112258110-112258128
36	FOSL1	chr5:112257764-112258135	H1-hESC	embryonic stem cell:	n/a	n/a
37	YY1	chr5:112257682-112258181	K562	blood:	n/a	chr5:112258098-112258107 chr5:112257715-112257726 chr5:112257960-112257971 chr5:112257717-112257731
38	SIN3A	chr5:112257728-112258227	GM12878	blood:	n/a	chr5:112258070-112258079
39	MYC	chr5:112257769-112258018	MCF-7	breast:	n/a	n/a
40	BHLHE40	chr5:112257784-112258307	GM12878	blood:	n/a	chr5:112257958-112257974
41	EGR1	chr5:112257783-112258354	ECC-1	luminal epithelium:	n/a	chr5:112258096-112258109 chr5:112258099-112258108 chr5:112258097-112258108 chr5:112258187-112258197 chr5:112258184-112258197 chr5:112258096-112258109 chr5:112258096-112258109 chr5:112258055-112258069 chr5:112258096-112258109 chr5:112258099-112258109
42	POLR2A	chr5:112256663-112258295	MCF-7	breast:	n/a	n/a
43	POLR2A	chr5:112257410-112258237	PFSK-1	brain:	n/a	n/a
44	RAD21	chr5:112257825-112258371	MCF-7	breast:	n/a	chr5:112258088-112258102
45	RAD21	chr5:112257897-112258282	HepG2	liver:	n/a	chr5:112258088-112258102
46	TAF1	chr5:112257671-112258160	GM12878	blood:	n/a	n/a
47	YY1	chr5:112257721-112258182	GM12892	blood:	n/a	chr5:112258098-112258107 chr5:112257960-112257971
48	REST	chr5:112257379-112258052	K562	blood:	n/a	chr5:112257534-112257544 chr5:112257910-112257930 chr5:112257705-112257725 chr5:112257709-112257722 chr5:112257712-112257725 chr5:112257706-112257724 chr5:112257705-112257725
49	POLR2A	chr5:112257661-112258205	U87	brain:	n/a	n/a
50	TCF7L2	chr5:112257802-112257935	PANC-1	pancreas:	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	chr5:112223765..112227904-chr5:112256681..112259724,3	K562	blood:
6	chr5:112195239..112200315-chr5:112255126..112261929,8	MCF-7	breast:
7	chr5:111496112..111498947-chr5:112256676..112259616,2	K562	blood:
8	chr5:112255209..112259355-chr5:112310614..112316433,9	K562	blood:
9	chr5:112196983..112197664-chr5:112257709..112258331,2	Hela-S3	cervix:

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

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs149130	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs149190	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs149191	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs149192	0.86[EUR][1000 genomes]
rs149193	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs151979	0.94[ASN][1000 genomes]
rs151980	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs153544	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs153551	0.83[EUR][1000 genomes]
rs153552	0.81[EUR][1000 genomes]
rs153553	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs153557	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs153559	0.87[EUR][1000 genomes]
rs153561	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153563	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153569	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs154344	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1644099	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17135222	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2545156	0.84[EUR][1000 genomes]
rs2545170	0.84[EUR][1000 genomes]
rs3317	0.86[EUR][1000 genomes]
rs351768	0.81[EUR][1000 genomes]
rs368575	0.85[EUR][1000 genomes]
rs410701	0.86[EUR][1000 genomes]
rs419155	0.86[EUR][1000 genomes]
rs448613	0.86[EUR][1000 genomes]
rs456531	0.86[EUR][1000 genomes]
rs460137	0.80[EUR][1000 genomes]
rs467660	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs468751	0.87[EUR][1000 genomes]
rs469523	0.85[ASN][1000 genomes]
rs469675	0.85[ASN][1000 genomes]
rs469753	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs469886	0.86[EUR][1000 genomes]
rs67293732	0.84[EUR][1000 genomes]
rs712670	0.85[EUR][1000 genomes]
rs818426	0.85[EUR][1000 genomes]
rs818428	0.87[EUR][1000 genomes]
rs818430	0.87[EUR][1000 genomes]
rs818797	0.85[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs153556	REEP5	Cis_1M	lymphoblastoid	RTeQTL

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	chr5:112256200-112258000	Active TSS	NHLF	lung
5	chr5:112256200-112258200	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr5:112256200-112258200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:112256200-112258200	Active TSS	GM12878-XiMat	blood
8	chr5:112256200-112258400	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr5:112256200-112258600	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr5:112256400-112258000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
11	chr5:112256400-112258000	Active TSS	Colonic Mucosa	Colon
12	chr5:112256400-112258200	Active TSS	H1 Cell Line	embryonic stem cell
13	chr5:112256400-112258200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:112256400-112258200	Active TSS	Placenta	Placenta
15	chr5:112256400-112258200	Active TSS	Gastric	stomach
16	chr5:112256400-112258200	Active TSS	Psoas Muscle	Psoas
17	chr5:112256400-112258200	Active TSS	HSMM	muscle
18	chr5:112256400-112258400	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr5:112256400-112258400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:112256400-112258400	Active TSS	H9 Cell Line	embryonic stem cell
21	chr5:112256400-112258400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:112256400-112258400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:112256400-112258400	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr5:112256400-112258400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:112256400-112258400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr5:112256400-112258400	Active TSS	Aorta	Aorta
27	chr5:112256400-112258400	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr5:112256400-112258400	Active TSS	Left Ventricle	heart
29	chr5:112256400-112258400	Active TSS	Ovary	ovary
30	chr5:112256400-112258400	Active TSS	Pancreas	Pancrea
31	chr5:112256400-112258400	Active TSS	Right Ventricle	heart
32	chr5:112256400-112258600	Active TSS	Fetal Muscle Trunk	muscle
33	chr5:112256600-112258000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:112256600-112258000	Active TSS	Small Intestine	intestine
35	chr5:112256600-112258200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:112256600-112258200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:112256600-112258200	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr5:112256600-112258200	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr5:112256600-112258200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:112256600-112258200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:112256600-112258200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr5:112256600-112258200	Active TSS	Brain Hippocampus Middle	brain
43	chr5:112256600-112258200	Active TSS	Brain Substantia Nigra	brain
44	chr5:112256600-112258200	Active TSS	Fetal Intestine Large	intestine
45	chr5:112256600-112258200	Active TSS	Fetal Stomach	stomach
46	chr5:112256600-112258200	Active TSS	Lung	lung
47	chr5:112256600-112258200	Active TSS	A549	lung
48	chr5:112256600-112258200	Active TSS	HMEC	breast
49	chr5:112256600-112258200	Active TSS	HSMMtube	muscle
50	chr5:112256600-112258200	Active TSS	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links