Variant report

Variant	rs2275092
Chromosome Location	chr6:150326267-150326268
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAET1L-2	chr6:150326209-150326280	NONHSAT115529

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11155692	0.89[ASN][1000 genomes]
rs11155693	0.89[ASN][1000 genomes]
rs11964763	0.88[ASN][1000 genomes]
rs11967324	0.86[ASN][1000 genomes]
rs11967376	0.89[ASN][1000 genomes]
rs11967392	0.89[ASN][1000 genomes]
rs11969666	0.89[ASN][1000 genomes]
rs11969681	0.89[ASN][1000 genomes]
rs13192866	0.89[ASN][1000 genomes]
rs13199630	0.89[ASN][1000 genomes]
rs13214660	0.89[ASN][1000 genomes]
rs1830833	0.89[ASN][1000 genomes]
rs1853666	0.97[ASN][1000 genomes]
rs1853667	0.97[ASN][1000 genomes]
rs1886363	0.83[ASN][1000 genomes]
rs1889553	0.81[ASN][1000 genomes]
rs1889554	0.83[ASN][1000 genomes]
rs2224893	0.89[ASN][1000 genomes]
rs2343265	0.87[ASN][1000 genomes]
rs3860819	0.89[ASN][1000 genomes]
rs3888034	0.91[ASN][1000 genomes]
rs3963990	1.00[ASN][1000 genomes]
rs4472362	0.87[ASN][1000 genomes]
rs6940683	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7739781	0.89[ASN][1000 genomes]
rs7762217	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9322232	0.89[ASN][1000 genomes]
rs9371624	1.00[ASN][1000 genomes]
rs9383996	0.88[ASN][1000 genomes]
rs9384002	0.89[ASN][1000 genomes]
rs9384003	0.89[ASN][1000 genomes]
rs9384010	0.89[ASN][1000 genomes]
rs9384011	0.89[ASN][1000 genomes]
rs9384030	1.00[ASN][1000 genomes]
rs9384033	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9397517	0.88[ASN][1000 genomes]
rs9397521	0.89[ASN][1000 genomes]
rs9397541	0.99[ASN][1000 genomes]
rs942513	0.87[ASN][1000 genomes]
rs942514	0.87[ASN][1000 genomes]
rs9478336	0.89[ASN][1000 genomes]
rs9478352	0.96[EUR][1000 genomes]
rs9479328	0.89[ASN][1000 genomes]
rs9479329	0.89[ASN][1000 genomes]
rs9479330	0.89[ASN][1000 genomes]
rs9479331	0.89[ASN][1000 genomes]
rs9479332	0.89[ASN][1000 genomes]
rs9479339	0.89[ASN][1000 genomes]
rs9479340	0.89[ASN][1000 genomes]
rs9479341	0.89[ASN][1000 genomes]
rs9479343	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv970176	chr6:150319173-150343329	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv7375	chr6:150324114-150388625	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3344440	chr6:150324131-150388650	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150325200-150327000	Active TSS	Hela-S3	cervix
2	chr6:150325400-150326400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
3	chr6:150325400-150327000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:150325400-150327000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
5	chr6:150325400-150327000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
6	chr6:150325400-150327000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:150325400-150327000	Flanking Active TSS	GM12878-XiMat	blood
8	chr6:150325400-150327200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr6:150325600-150326400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr6:150325600-150326400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:150325600-150326400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
12	chr6:150325600-150326400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
13	chr6:150325600-150326800	Flanking Active TSS	HMEC	breast
14	chr6:150325600-150327000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr6:150325600-150327000	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr6:150325600-150327000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr6:150325600-150327000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:150325600-150327000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:150325600-150327000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:150325600-150327000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
21	chr6:150325600-150327000	Active TSS	Right Ventricle	heart
22	chr6:150325600-150327000	Bivalent/Poised TSS	Thymus	Thymus
23	chr6:150325600-150327200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr6:150325600-150327200	Active TSS	A549	lung
25	chr6:150325600-150327200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
26	chr6:150325600-150327400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:150325800-150326400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:150325800-150326400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
29	chr6:150325800-150326600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:150325800-150326800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:150325800-150326800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:150325800-150326800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
33	chr6:150325800-150326800	Active TSS	Muscle Satellite Cultured Cells	--
34	chr6:150325800-150326800	Active TSS	Aorta	Aorta
35	chr6:150325800-150326800	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr6:150325800-150327000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr6:150325800-150327000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:150325800-150327000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:150325800-150327000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:150325800-150327000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:150325800-150327000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
42	chr6:150325800-150327000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:150325800-150327000	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr6:150325800-150327000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:150325800-150327000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:150325800-150327000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
47	chr6:150325800-150327000	Active TSS	Left Ventricle	heart
48	chr6:150325800-150327000	Active TSS	Psoas Muscle	Psoas
49	chr6:150325800-150327000	Active TSS	NHLF	lung
50	chr6:150325800-150327200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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