Variant report

Variant	rs12344019
Chromosome Location	chr9:26880240-26880241
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLAA-2	chr9:26880176-26880547	NONHSAT130599

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10812483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10812484	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10967568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10967574	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10967577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10967579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10967582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10967583	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10967584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12004912	0.93[AFR][1000 genomes]
rs12335922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12336610	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12337566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12338827	0.99[AFR][1000 genomes]
rs12342214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12343057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12343845	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12343965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12344293	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12345414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12345417	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12345714	0.92[AFR][1000 genomes]
rs12346378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12351014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12351117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12351187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12352229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12352731	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12352777	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12353080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12353172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1414799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16910832	0.82[AFR][1000 genomes]
rs16910834	0.83[AFR][1000 genomes]
rs7023459	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7025993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7026496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7029328	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7035029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7039799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7851035	0.87[AFR][1000 genomes];1.00[AMR][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	nsv1026827	chr9:26693515-26904699	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv982204	chr9:26878626-26880449	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26822200-26889400	Weak transcription	Psoas Muscle	Psoas
2	chr9:26834000-26882400	Weak transcription	HUVEC	blood vessel
3	chr9:26834200-26882200	Weak transcription	HMEC	breast
4	chr9:26834200-26888200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr9:26834200-26891200	Weak transcription	NHDF-Ad	bronchial
6	chr9:26836600-26891400	Weak transcription	Brain Substantia Nigra	brain
7	chr9:26840600-26882400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr9:26842600-26882200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:26846600-26881600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr9:26847000-26883000	Weak transcription	K562	blood
11	chr9:26851400-26888000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr9:26851800-26888600	Weak transcription	Fetal Heart	heart
13	chr9:26851800-26891600	Weak transcription	Stomach Mucosa	stomach
14	chr9:26852400-26888000	Weak transcription	NHLF	lung
15	chr9:26855000-26882200	Weak transcription	Right Ventricle	heart
16	chr9:26855800-26888200	Weak transcription	NH-A	brain
17	chr9:26856000-26881600	Weak transcription	Brain Hippocampus Middle	brain
18	chr9:26856000-26882200	Weak transcription	Brain Anterior Caudate	brain
19	chr9:26856000-26882200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr9:26856200-26881400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr9:26856600-26888400	Weak transcription	Osteobl	bone
22	chr9:26857600-26891000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr9:26859400-26882200	Weak transcription	Small Intestine	intestine
24	chr9:26859600-26881400	Weak transcription	HSMMtube	muscle
25	chr9:26859800-26880400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr9:26859800-26890000	Weak transcription	Colon Smooth Muscle	Colon
27	chr9:26871200-26882200	Weak transcription	Hela-S3	cervix
28	chr9:26872400-26880800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr9:26873400-26881400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:26875600-26882200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr9:26875600-26882200	Strong transcription	Liver	Liver
32	chr9:26875600-26882200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr9:26875600-26882400	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:26875600-26885000	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr9:26875800-26881800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr9:26875800-26887400	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr9:26876000-26881600	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr9:26876000-26881800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:26876000-26882200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr9:26876400-26881400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr9:26876400-26882200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr9:26876600-26882200	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr9:26876800-26881600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:26876800-26882000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr9:26876800-26887400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr9:26876800-26888400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr9:26877400-26883400	Strong transcription	Adipose Nuclei	Adipose
48	chr9:26877400-26885000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr9:26878000-26880400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr9:26878000-26881800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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