Variant report

Variant	rs12347380
Chromosome Location	chr9:15224499-15224500
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSIP1-3	chr9:15224358-15224503	NONHSAT130261

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10121353	1.00[AMR][1000 genomes]
rs10124400	1.00[ASN][1000 genomes]
rs12005901	1.00[AMR][1000 genomes]
rs12337646	1.00[AMR][1000 genomes]
rs12341643	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28729420	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs525147	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs535659	0.83[AMR][1000 genomes]
rs548264	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs563044	1.00[ASN][1000 genomes]
rs603033	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031340	chr9:15163004-15332769	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv521191	chr9:15218947-15246652	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15163000-15233000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:15171000-15228600	Weak transcription	Stomach Mucosa	stomach
3	chr9:15182200-15229200	Weak transcription	Gastric	stomach
4	chr9:15185600-15225800	Weak transcription	Pancreas	Pancrea
5	chr9:15192200-15229200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr9:15193400-15249600	Weak transcription	Colonic Mucosa	Colon
7	chr9:15197200-15225000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr9:15206000-15229200	Weak transcription	Ovary	ovary
9	chr9:15207600-15225600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr9:15210000-15231800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr9:15210600-15226200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:15211400-15229000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr9:15211400-15229000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr9:15211600-15224600	Weak transcription	NHEK	skin
15	chr9:15211600-15226600	Weak transcription	HMEC	breast
16	chr9:15212000-15224800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:15212000-15225400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr9:15212400-15225600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:15212800-15226000	Weak transcription	Liver	Liver
20	chr9:15213600-15225800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr9:15214800-15226000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr9:15215400-15227400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:15219400-15225000	Strong transcription	Primary T cells from cord blood	blood
24	chr9:15220000-15225200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr9:15220000-15229200	Weak transcription	Fetal Kidney	kidney
26	chr9:15220000-15229200	Weak transcription	Small Intestine	intestine
27	chr9:15220400-15224600	Strong transcription	Fetal Intestine Large	intestine
28	chr9:15220400-15225200	Weak transcription	Psoas Muscle	Psoas
29	chr9:15221200-15225800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:15221200-15229200	Weak transcription	Aorta	Aorta
31	chr9:15221200-15242200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:15221600-15226600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr9:15221800-15231200	Weak transcription	Fetal Intestine Small	intestine
34	chr9:15221800-15233000	Weak transcription	Osteobl	bone
35	chr9:15221800-15242800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:15222000-15224600	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr9:15222000-15225000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr9:15222000-15226800	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr9:15222200-15224600	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr9:15222200-15225400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:15222400-15224600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr9:15222400-15225200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr9:15222600-15224600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr9:15222600-15225000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr9:15222600-15225200	Strong transcription	HepG2	liver
46	chr9:15222600-15225400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr9:15222600-15230200	Weak transcription	Left Ventricle	heart
48	chr9:15222800-15226000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr9:15223000-15224600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr9:15223000-15224600	Strong transcription	Duodenum Mucosa	Duodenum

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