Variant report

Variant	rs62007339
Chromosome Location	chr15:77774510-77774511
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMG20A-6	chr15:77774392-77777949	NONHSAT047442

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10519165	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519166	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898506	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898522	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901298	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905548	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905890	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906093	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906155	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906220	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909547	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909771	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910225	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911362	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12912739	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12914885	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917103	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917143	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917211	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917347	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917359	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968817	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968829	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968848	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968851	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17384857	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17386174	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17469938	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471280	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471809	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17472416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1949269	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036896	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864841	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34023254	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34137991	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34158220	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34197100	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34237392	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34344208	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34410684	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34607003	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34660075	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34664675	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34665451	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34690222	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34772392	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34858590	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34905779	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34918566	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35015654	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35277326	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35347401	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35383172	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35420345	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35450609	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35628983	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35775156	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35778082	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35834995	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35892909	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36103772	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4288963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4349115	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007266	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007269	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007278	0.89[ASN][1000 genomes]
rs62007303	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007307	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007310	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007313	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007316	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007337	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007338	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007340	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62007343	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010561	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010567	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72742499	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031202	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907399	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62007339	SGK269	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77750400-77777800	Strong transcription	Primary B cells from peripheral blood	blood
2	chr15:77750600-77777800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr15:77750600-77779200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:77750600-77779600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:77750800-77780400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:77753400-77777600	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr15:77755200-77775600	Strong transcription	Duodenum Mucosa	Duodenum
8	chr15:77755400-77777800	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr15:77756200-77778400	Strong transcription	Fetal Thymus	thymus
10	chr15:77756800-77775800	Weak transcription	Pancreas	Pancrea
11	chr15:77759200-77776000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:77761600-77775800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr15:77762000-77775800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr15:77764600-77774800	Weak transcription	Fetal Brain Male	brain
15	chr15:77764600-77775400	Weak transcription	Brain Germinal Matrix	brain
16	chr15:77765200-77775400	Weak transcription	Right Ventricle	heart
17	chr15:77767200-77777400	Strong transcription	GM12878-XiMat	blood
18	chr15:77767600-77777600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr15:77769400-77774600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:77769400-77777600	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr15:77769400-77777600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr15:77769400-77777800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr15:77769400-77777800	Strong transcription	HepG2	liver
24	chr15:77769400-77778000	Strong transcription	Dnd41	blood
25	chr15:77769400-77779800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:77769600-77777600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:77769600-77777600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:77769600-77778000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr15:77769600-77778600	Strong transcription	Liver	Liver
30	chr15:77769800-77777600	Strong transcription	Primary hematopoietic stem cells	blood
31	chr15:77769800-77777800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:77769800-77777800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:77769800-77778000	Strong transcription	Primary T cells from cord blood	blood
34	chr15:77770000-77774600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:77770000-77777600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr15:77770000-77789200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr15:77770400-77777600	Strong transcription	Thymus	Thymus
38	chr15:77770600-77774600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:77770800-77775000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr15:77770800-77775400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:77771000-77775400	Weak transcription	Esophagus	oesophagus
42	chr15:77771000-77775400	Weak transcription	Gastric	stomach
43	chr15:77771000-77775400	Weak transcription	Lung	lung
44	chr15:77771000-77775400	Weak transcription	Right Atrium	heart
45	chr15:77771000-77775400	Weak transcription	Spleen	Spleen
46	chr15:77771000-77775600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:77771000-77775800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:77771000-77775800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr15:77771000-77775800	Weak transcription	Aorta	Aorta
50	chr15:77771200-77775000	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links