Variant report

Variant	rs9589207
Chromosome Location	chr13:92003589-92003590
allele	A/G
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:6)
LncRNA
region (count:4)
Mature miRNA
region (count: 1)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:92002651..92004198-chr20:47895031..47896650,2	K562	blood:
2	chr11:65685854..65687838-chr13:92002138..92004111,2	K562	blood:
3	chr13:92002897..92004499-chr6:30582466..30585246,2	K562	blood:
4	chr11:65190238..65193171-chr13:92003562..92006013,2	K562	blood:
5	chr11:64007679..64009892-chr13:92001604..92004305,2	K562	blood:
6	chr13:92002065..92004050-chr19:46274195..46275791,2	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPC5-1	chr13:92003568-92003645	ENSG00000243108
2	lnc-GPC5-1	chr13:92001952-92004656	ENSG00000215417.5
3	lnc-GPC5-1	chr13:92001952-92006829	NONHSAT034665
4	lnc-GPC5-1	chr13:92002410-92004350	ENSG00000215417.5

miRNA name	Chromosome Location	mirBase accession
hsa-miR-92a-1-5p	chr13:92003578-92003600	MIMAT0004507

No data

Variant related genes	Relation type
ENSG00000204569	Chromatin interaction
ENSG00000175573	Chromatin interaction
ENSG00000267395	Chromatin interaction
ENSG00000209042	Chromatin interaction
ENSG00000175550	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000173486	Chromatin interaction
ENSG00000177410	Chromatin interaction
ENSG00000104936	Chromatin interaction
ZWINT	Mature miRNA region
MRPS11	Mature miRNA region
GTPBP4	Mature miRNA region
EEF2	Mature miRNA region
SLC2A4	Mature miRNA region
IQSEC1	Mature miRNA region
TUBB	Mature miRNA region
PLK1	Mature miRNA region
RPL29	Mature miRNA region
MBLAC2	Mature miRNA region
UBB	Mature miRNA region
RAD51	Mature miRNA region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12323299	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16945806	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16945815	0.87[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16945820	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28729540	1.00[AMR][1000 genomes]
rs3848048	1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs7988366	1.00[AMR][1000 genomes]
rs9583916	1.00[AMR][1000 genomes]
rs9583917	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9589194	1.00[AMR][1000 genomes]
rs9589204	0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9589205	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9589208	0.87[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9589216	1.00[AMR][1000 genomes]
rs9989081	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042947	chr13:91571040-92416897	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
2	nsv541871	chr13:91571040-92416897	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
3	esv1803618	chr13:91669587-92277699	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1945 gene(s)	inside rSNPs	diseases
4	nsv1050259	chr13:91759549-92152078	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
5	nsv541872	chr13:91759549-92152078	Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
6	nsv832679	chr13:91859467-92030220	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1943 gene(s)	inside rSNPs	diseases
7	esv1795019	chr13:91992157-92003589	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1146 gene(s)	inside rSNPs	diseases
8	esv1796361	chr13:91999737-92003589	Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1145 gene(s)	inside rSNPs	diseases
9	esv1802358	chr13:91999737-92003589	Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1145 gene(s)	inside rSNPs	diseases
10	esv1802567	chr13:91999737-92003589	Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1145 gene(s)	inside rSNPs	diseases
11	esv1808768	chr13:91999737-92003589	Active TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1145 gene(s)	inside rSNPs	diseases
12	esv1815968	chr13:91999737-92003589	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1145 gene(s)	inside rSNPs	diseases
13	esv1834079	chr13:91999737-92003589	Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1145 gene(s)	inside rSNPs	diseases
14	esv1834506	chr13:91999737-92003589	Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1145 gene(s)	inside rSNPs	diseases
15	esv1839472	chr13:91999737-92003589	Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1145 gene(s)	inside rSNPs	diseases
16	esv1840965	chr13:91999737-92003589	Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1145 gene(s)	inside rSNPs	diseases
17	esv1802171	chr13:91999737-92015977	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1940 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:92001400-92004200	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
2	chr13:92001400-92004400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
3	chr13:92001400-92004400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
4	chr13:92001400-92004600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
5	chr13:92001400-92004600	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr13:92001400-92004800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
7	chr13:92001400-92005000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
8	chr13:92001400-92005000	Transcr. at gene 5' and 3'	K562	blood
9	chr13:92001400-92005800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
10	chr13:92001600-92003600	Transcr. at gene 5' and 3'	NHEK	skin
11	chr13:92001600-92003800	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
12	chr13:92001600-92003800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:92001600-92004600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
14	chr13:92001600-92010200	Weak transcription	Spleen	Spleen
15	chr13:92001600-92010800	Weak transcription	Pancreas	Pancrea
16	chr13:92001600-92012200	Weak transcription	Esophagus	oesophagus
17	chr13:92001800-92003600	Transcr. at gene 5' and 3'	A549	lung
18	chr13:92001800-92003800	Transcr. at gene 5' and 3'	Hela-S3	cervix
19	chr13:92001800-92004000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr13:92001800-92004800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr13:92001800-92007000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr13:92001800-92015600	Weak transcription	Ovary	ovary
23	chr13:92001800-92027200	Weak transcription	Aorta	Aorta
24	chr13:92002000-92003600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr13:92002000-92003600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr13:92002000-92003800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr13:92002000-92003800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
28	chr13:92002000-92004600	Genic enhancers	Fetal Lung	lung
29	chr13:92002000-92005800	Weak transcription	Stomach Mucosa	stomach
30	chr13:92002000-92008400	Strong transcription	Placenta	Placenta
31	chr13:92002000-92011000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr13:92002000-92011200	Weak transcription	Colonic Mucosa	Colon
33	chr13:92002000-92012200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr13:92002200-92003600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr13:92002200-92003600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr13:92002200-92003600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
37	chr13:92002200-92003600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr13:92002200-92003600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr13:92002200-92003600	Transcr. at gene 5' and 3'	Liver	Liver
40	chr13:92002200-92003600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
41	chr13:92002200-92003800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr13:92002200-92003800	Transcr. at gene 5' and 3'	HMEC	breast
43	chr13:92002200-92007200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
44	chr13:92002200-92008400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr13:92002200-92008800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr13:92002200-92010800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr13:92002400-92003600	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
48	chr13:92002400-92003600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr13:92002400-92003600	Genic enhancers	Fetal Heart	heart
50	chr13:92002400-92003600	Genic enhancers	Fetal Muscle Leg	muscle

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