Variant report

Variant	rs153565
Chromosome Location	chr5:112250376-112250377
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112249716..112252598-chr5:112302249..112303940,2	MCF-7	breast:
2	chr5:112248880..112253416-chr5:112311841..112314795,5	K562	blood:
3	chr5:112243670..112246215-chr5:112250359..112252946,2	K562	blood:

Variant related genes	Relation type
ENSG00000172795	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1093611	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs153544	0.81[AMR][1000 genomes]
rs154344	0.81[AMR][1000 genomes]
rs430665	0.81[EUR][1000 genomes]
rs454968	0.82[EUR][1000 genomes]
rs455412	0.81[EUR][1000 genomes]
rs458451	0.81[EUR][1000 genomes]
rs459102	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs460832	0.81[EUR][1000 genomes]
rs468101	0.85[EUR][1000 genomes]
rs468610	0.87[EUR][1000 genomes]
rs468854	0.87[EUR][1000 genomes]
rs469727	0.87[EUR][1000 genomes]
rs469827	0.87[EUR][1000 genomes]
rs698405	0.85[EUR][1000 genomes]
rs712662	0.81[EUR][1000 genomes]
rs712663	0.82[AMR][1000 genomes]
rs712665	0.81[EUR][1000 genomes]
rs818429	0.82[AMR][1000 genomes];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	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
rs153565	SRP19	Cis_1M	lymphoblastoid	RTeQTL
rs153565	REEP5	cis	Esophagus Muscularis	GTEx

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	chr5:112229600-112256600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:112230200-112251600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:112237400-112254000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:112238200-112251600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr5:112238400-112251800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:112238400-112252800	Weak transcription	Small Intestine	intestine
17	chr5:112238400-112253800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr5:112241200-112250400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:112242200-112254200	Weak transcription	Fetal Kidney	kidney
20	chr5:112242400-112252800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:112242600-112256800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr5:112243200-112251400	Weak transcription	Brain Angular Gyrus	brain
23	chr5:112243200-112254000	Weak transcription	Fetal Brain Male	brain
24	chr5:112243400-112252800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:112244600-112251600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr5:112245800-112252000	Weak transcription	Fetal Brain Female	brain
27	chr5:112245800-112252400	Weak transcription	Fetal Thymus	thymus
28	chr5:112245800-112252800	Weak transcription	Colonic Mucosa	Colon
29	chr5:112245800-112253200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr5:112245800-112253200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:112246000-112251400	Weak transcription	Fetal Lung	lung
32	chr5:112246000-112254000	Weak transcription	Esophagus	oesophagus
33	chr5:112246000-112254000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr5:112246200-112254000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr5:112246400-112251400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr5:112246400-112251600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr5:112246600-112250400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr5:112246600-112251200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:112246600-112251800	Weak transcription	Colon Smooth Muscle	Colon
40	chr5:112246600-112252000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr5:112246800-112251000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr5:112246800-112251600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr5:112246800-112251800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr5:112246800-112253400	Weak transcription	Psoas Muscle	Psoas
45	chr5:112247000-112251000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr5:112247000-112251800	Weak transcription	Brain Anterior Caudate	brain
47	chr5:112247000-112252600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:112247200-112250800	Weak transcription	HMEC	breast
49	chr5:112247200-112251200	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr5:112247200-112251200	Weak transcription	Fetal Intestine Large	intestine

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