Variant report

Variant	rs62439784
Chromosome Location	chr6:149913584-149913585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149910172..149914647-chr6:149914735..149918392,5	K562	blood:

Variant related genes	Relation type
ENSG00000202343	Chromatin interaction
ENSG00000220848	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10747275	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10782310	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10782311	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10782312	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10782313	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1080670	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11155662	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11155668	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11155669	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11155670	0.90[AMR][1000 genomes]
rs11155671	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12174716	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12183664	0.86[AMR][1000 genomes]
rs12191643	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12193364	0.85[AMR][1000 genomes]
rs12201033	0.81[AMR][1000 genomes]
rs12206402	0.84[AMR][1000 genomes]
rs12523793	0.81[AMR][1000 genomes]
rs12529698	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12662162	0.81[EUR][1000 genomes]
rs12662174	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2064520	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2064521	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3734295	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3777949	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4869812	0.81[AMR][1000 genomes]
rs4870139	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4870144	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4870267	0.81[AMR][1000 genomes]
rs55849538	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55993747	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56091542	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57938011	0.84[AMR][1000 genomes]
rs58189451	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62439811	0.84[AMR][1000 genomes]
rs62439836	0.81[AMR][1000 genomes]
rs66516768	0.81[AMR][1000 genomes]
rs7381555	0.83[AMR][1000 genomes]
rs7740278	0.87[AMR][1000 genomes]
rs9027	0.81[EUR][1000 genomes]
rs9285521	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9285522	0.86[AMR][1000 genomes]
rs9285523	0.84[AMR][1000 genomes]
rs9322189	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9322190	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9322192	0.81[EUR][1000 genomes]
rs9322193	0.82[EUR][1000 genomes]
rs9322194	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9322196	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9322197	0.80[EUR][1000 genomes]
rs9322198	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9322199	0.84[AMR][1000 genomes]
rs9322200	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9322204	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9322207	0.86[AMR][1000 genomes]
rs9322208	0.86[AMR][1000 genomes]
rs9377228	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9377229	0.82[EUR][1000 genomes]
rs9377230	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9379314	0.87[AMR][1000 genomes]
rs9379348	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9393132	0.89[AMR][1000 genomes]
rs9399692	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9399693	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9404047	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9404048	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9406286	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9406345	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9406346	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9485405	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9485408	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9498382	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9498384	0.85[EUR][1000 genomes]
rs9505823	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9505824	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9505982	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9688452	0.86[AMR][1000 genomes]
rs9688794	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9688861	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9689084	0.87[AMR][1000 genomes]
rs9689599	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9689716	0.88[AMR][1000 genomes]
rs9689723	0.89[AMR][1000 genomes]
rs9718079	0.86[AMR][1000 genomes]
rs9766037	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9766886	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9767105	0.89[AMR][1000 genomes]
rs9767123	0.87[AMR][1000 genomes]
rs9767554	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9767555	0.85[AMR][1000 genomes]
rs9767713	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9800580	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9800603	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9800614	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9800686	0.81[AMR][1000 genomes]
rs9800736	0.83[AMR][1000 genomes]
rs9800871	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9968911	0.87[AMR][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	nsv289	chr6:149864898-149998818	Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv5534	chr6:149864898-149998818	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv886762	chr6:149866452-150174507	Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv1794633	chr6:149903597-149944908	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1792620	chr6:149909491-150083621	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs62439784	RAET1G	cis	Thyroid	GTEx
rs62439784	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs62439784	RP11-350J20.5	cis	lung	GTEx
rs62439784	RP11-350J20.5	cis	Esophagus Mucosa	GTEx
rs62439784	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs62439784	RAET1G	cis	Artery Tibial	GTEx
rs62439784	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs62439784	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs62439784	RP11-350J20.5	cis	Adipose Subcutaneous	GTEx
rs62439784	RP11-350J20.5	cis	Artery Tibial	GTEx
rs62439784	LRP11	cis	Skin Sun Exposed Lower leg	GTEx
rs62439784	GINM1	cis	Whole Blood	GTEx
rs62439784	RP11-350J20.5	cis	Thyroid	GTEx
rs62439784	RP11-350J20.5	cis	Esophagus Muscularis	GTEx
rs62439784	RP11-350J20.5	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149888600-149922000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:149888800-149914800	Weak transcription	A549	lung
3	chr6:149889000-149928000	Weak transcription	Stomach Mucosa	stomach
4	chr6:149889200-149919600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr6:149889400-149924200	Weak transcription	Fetal Heart	heart
6	chr6:149889600-149914200	Weak transcription	Hela-S3	cervix
7	chr6:149889600-149931400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr6:149893800-149926600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr6:149894200-149920000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:149895600-149923200	Strong transcription	Dnd41	blood
11	chr6:149898400-149919200	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:149898600-149927400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:149898800-149913800	Weak transcription	Right Ventricle	heart
14	chr6:149899200-149915000	Weak transcription	Esophagus	oesophagus
15	chr6:149899200-149929800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:149900200-149926800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:149900400-149923200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:149901000-149919200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:149901000-149920200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:149901000-149923200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr6:149901000-149923200	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr6:149901200-149920000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:149901600-149919800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:149901800-149919400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr6:149902200-149915200	Weak transcription	HMEC	breast
26	chr6:149902200-149920200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:149902800-149929000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:149903200-149914200	Weak transcription	NHEK	skin
29	chr6:149903200-149915000	Weak transcription	Gastric	stomach
30	chr6:149903800-149914200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr6:149903800-149914200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr6:149903800-149924200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:149904200-149914200	Weak transcription	Fetal Kidney	kidney
34	chr6:149904400-149914000	Weak transcription	Colonic Mucosa	Colon
35	chr6:149905200-149926200	Strong transcription	Fetal Stomach	stomach
36	chr6:149905400-149919400	Strong transcription	Left Ventricle	heart
37	chr6:149905400-149920000	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:149906000-149918800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:149906800-149922800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:149907000-149919600	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr6:149907000-149925800	Strong transcription	Fetal Thymus	thymus
42	chr6:149907400-149916400	Strong transcription	Stomach Smooth Muscle	stomach
43	chr6:149907400-149918000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr6:149907600-149925800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:149909000-149914000	Weak transcription	Thymus	Thymus
46	chr6:149909000-149914200	Weak transcription	NHLF	lung
47	chr6:149909000-149914800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:149909000-149915000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:149909000-149915000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr6:149909000-149915000	Weak transcription	Pancreas	Pancrea

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