Variant report

Variant	rs153562
Chromosome Location	chr5:112253119-112253120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:112246563..112249281-chr5:112250414..112253168,3	K562	blood:
2	chr5:112248880..112253416-chr5:112311841..112314795,5	K562	blood:
3	chr5:112252458..112254818-chr5:112292295..112294312,2	K562	blood:
4	chr5:112253073..112255997-chr5:112284078..112285645,2	K562	blood:
5	chr5:112252465..112254297-chr5:112272394..112274579,2	K562	blood:
6	chr5:112030572..112032365-chr5:112252746..112254378,2	K562	blood:
7	chr5:112243328..112246108-chr5:112252960..112255177,2	MCF-7	breast:
8	chr5:112252495..112254832-chr5:112301145..112303115,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000172795	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1069061	0.82[AMR][1000 genomes]
rs1093677	0.82[AMR][1000 genomes]
rs149192	0.94[ASN][1000 genomes]
rs149502	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs151976	0.82[AMR][1000 genomes]
rs151977	0.82[AMR][1000 genomes]
rs151978	0.82[AMR][1000 genomes]
rs153545	0.82[AMR][1000 genomes]
rs153558	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs153559	0.93[ASN][1000 genomes]
rs153568	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs153570	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs173466	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs193527	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2545166	0.82[AMR][1000 genomes]
rs2545167	0.82[AMR][1000 genomes]
rs2909904	0.81[AMR][1000 genomes]
rs372492	0.82[AMR][1000 genomes]
rs380144	0.81[AMR][1000 genomes]
rs382260	0.82[AMR][1000 genomes]
rs430665	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs431287	0.82[AMR][1000 genomes]
rs434090	0.82[AMR][1000 genomes]
rs438252	0.85[AMR][1000 genomes]
rs439456	0.84[AMR][1000 genomes]
rs455412	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs455469	0.82[AMR][1000 genomes]
rs458451	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs459102	0.80[EUR][1000 genomes]
rs460301	0.81[AMR][1000 genomes]
rs460832	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs461424	0.85[AMR][1000 genomes]
rs461866	0.82[AMR][1000 genomes]
rs463229	0.83[AMR][1000 genomes]
rs468101	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs468610	0.81[EUR][1000 genomes]
rs468783	0.82[AMR][1000 genomes]
rs468854	0.82[EUR][1000 genomes]
rs469523	0.82[EUR][1000 genomes]
rs469663	0.82[AMR][1000 genomes]
rs469702	0.82[EUR][1000 genomes]
rs469716	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs469727	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs469760	0.82[AMR][1000 genomes]
rs469827	0.82[EUR][1000 genomes]
rs481789	0.81[AMR][1000 genomes]
rs497844	0.83[AMR][1000 genomes]
rs565453	0.83[AMR][1000 genomes]
rs565603	0.82[AMR][1000 genomes]
rs698405	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs712662	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs712664	0.82[AMR][1000 genomes]
rs712665	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs712666	0.85[AMR][1000 genomes]
rs712668	0.83[AMR][1000 genomes]
rs712671	0.85[AMR][1000 genomes]
rs818424	0.81[AMR][1000 genomes]
rs818427	0.83[AMR][1000 genomes]
rs818429	0.80[EUR][1000 genomes]
rs864682	0.81[AMR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs153562	SRP19	Cis_1M	lymphoblastoid	RTeQTL

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	chr5:112215200-112255800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:112221800-112256600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:112222000-112256400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:112223000-112256400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:112223000-112256600	Weak transcription	Thymus	Thymus
8	chr5:112229600-112256600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:112237400-112254000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:112238400-112253800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr5:112242200-112254200	Weak transcription	Fetal Kidney	kidney
12	chr5:112242600-112256800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:112243200-112254000	Weak transcription	Fetal Brain Male	brain
14	chr5:112245800-112253200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr5:112245800-112253200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr5:112246000-112254000	Weak transcription	Esophagus	oesophagus
17	chr5:112246000-112254000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr5:112246200-112254000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr5:112246800-112253400	Weak transcription	Psoas Muscle	Psoas
20	chr5:112247800-112255800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:112248000-112255600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:112248200-112255600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:112248400-112256000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:112249200-112254000	Strong transcription	Placenta	Placenta
25	chr5:112249400-112254200	Strong transcription	Liver	Liver
26	chr5:112249400-112254400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr5:112249400-112255600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr5:112249600-112254200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:112250000-112254600	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr5:112250200-112254000	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr5:112250200-112254400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:112250200-112254800	Genic enhancers	Brain Inferior Temporal Lobe	brain
33	chr5:112250400-112253200	Weak transcription	Gastric	stomach
34	chr5:112250400-112253800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:112250400-112253800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:112250400-112254000	Weak transcription	Stomach Mucosa	stomach
37	chr5:112250400-112254200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr5:112250600-112253200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr5:112250600-112254000	Weak transcription	Spleen	Spleen
40	chr5:112250800-112253200	Weak transcription	NHLF	lung
41	chr5:112250800-112254000	Strong transcription	NHEK	skin
42	chr5:112250800-112255400	Strong transcription	HMEC	breast
43	chr5:112251000-112256000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr5:112251200-112253200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:112251200-112253200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr5:112251200-112255800	Strong transcription	A549	lung
47	chr5:112251200-112256000	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr5:112251200-112256000	Genic enhancers	Primary T cells fromperipheralblood	blood
49	chr5:112251200-112256200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr5:112251400-112253200	Strong transcription	Fetal Lung	lung

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