Variant report

Variant	rs153553
Chromosome Location	chr5:112261278-112261279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112255914..112262078-chr5:112308752..112315375,16	MCF-7	breast:
2	chr5:112258754..112260468-chr5:112260829..112262760,2	MCF-7	breast:
3	chr5:112195239..112200315-chr5:112255126..112261929,8	MCF-7	breast:
4	chr5:112257953..112260534-chr5:112261004..112262710,2	K562	blood:

Variant related genes	Relation type
ENSG00000172795	Chromatin interaction
ENSG00000153037	Chromatin interaction
ENSG00000272869	Chromatin interaction
ENSG00000129625	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs149130	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs149190	0.91[ASN][1000 genomes]
rs149191	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs149192	0.82[EUR][1000 genomes]
rs151979	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs151980	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs153544	0.81[AMR][1000 genomes]
rs153556	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs153557	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs153559	0.83[EUR][1000 genomes]
rs153561	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs153563	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs153569	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs154344	0.81[AMR][1000 genomes]
rs1644099	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17135222	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs467660	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs469523	0.88[ASN][1000 genomes]
rs469675	0.88[ASN][1000 genomes]
rs469753	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs818799	0.81[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs153553	REEP5	cis	Esophagus Muscularis	GTEx
rs153553	REEP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112258000-112265000	Weak transcription	Small Intestine	intestine
2	chr5:112258400-112287400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:112258600-112264000	Weak transcription	A549	lung
4	chr5:112258600-112264200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:112258800-112263600	Weak transcription	Fetal Intestine Small	intestine
6	chr5:112259000-112263400	Weak transcription	Hela-S3	cervix
7	chr5:112259000-112267200	Weak transcription	Psoas Muscle	Psoas
8	chr5:112259000-112267200	Weak transcription	Right Atrium	heart
9	chr5:112259000-112269200	Weak transcription	Osteobl	bone
10	chr5:112259200-112262000	Weak transcription	Fetal Brain Male	brain
11	chr5:112259400-112261400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr5:112259400-112261600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:112259400-112264000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr5:112259600-112261600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr5:112259600-112265000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:112259600-112267600	Enhancers	Primary B cells from peripheral blood	blood
17	chr5:112259800-112262600	Weak transcription	Primary T cells from cord blood	blood
18	chr5:112259800-112262600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:112259800-112263000	Weak transcription	Placenta	Placenta
20	chr5:112259800-112265200	Enhancers	Primary B cells from cord blood	blood
21	chr5:112260000-112261400	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr5:112260000-112262600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr5:112260000-112262800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr5:112260000-112263000	Weak transcription	Fetal Thymus	thymus
25	chr5:112260000-112263200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr5:112260000-112263200	Weak transcription	Dnd41	blood
27	chr5:112260200-112262400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr5:112260200-112263000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr5:112260200-112263400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr5:112260200-112263800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr5:112260200-112264000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr5:112260400-112262600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr5:112260400-112262600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr5:112260400-112267000	Weak transcription	K562	blood
35	chr5:112260600-112262200	Enhancers	GM12878-XiMat	blood
36	chr5:112260600-112262400	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr5:112260600-112263400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr5:112261200-112261400	Enhancers	Primary hematopoietic stem cells	blood
39	chr5:112261200-112262400	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr5:112261200-112263200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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