Variant report

Variant	rs830706
Chromosome Location	chr16:12279574-12279575
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	chr16:12264911..12267612-chr16:12276958..12279714,2	K562	blood:
2	chr16:12272777..12275481-chr16:12278780..12280822,3	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11642667	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1701111	0.90[AMR][1000 genomes]
rs1704094	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1704130	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2456272	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2968353	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs709418	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709419	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709420	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709421	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs709422	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8062913	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs830696	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs830698	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs830700	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs830701	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs830704	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs830705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs830707	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs830708	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs830709	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs830710	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs830724	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs830725	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs844224	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs844225	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs853869	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs853870	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs862692	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs865533	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs866180	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs905952	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs937965	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9934120	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[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	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1052973	chr16:12188092-12307880	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1039590	chr16:12237623-12279574	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv571461	chr16:12268830-12314451	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs830706	GRIN2A	cis	parietal	SCAN
rs830706	PARN	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12242200-12299400	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr16:12242400-12280600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr16:12257000-12296800	Weak transcription	Thymus	Thymus
4	chr16:12261200-12293400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr16:12261200-12293600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr16:12261400-12292400	Weak transcription	GM12878-XiMat	blood
7	chr16:12261800-12322000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr16:12262600-12282200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr16:12263200-12287600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr16:12268400-12280800	Weak transcription	Lung	lung
11	chr16:12268800-12280200	Weak transcription	HepG2	liver
12	chr16:12271400-12293600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr16:12272200-12280400	Weak transcription	NHDF-Ad	bronchial
14	chr16:12272200-12282200	Weak transcription	Right Atrium	heart
15	chr16:12272400-12280200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr16:12272400-12281800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr16:12272400-12282600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr16:12272400-12282600	Weak transcription	Ovary	ovary
19	chr16:12272600-12282400	Weak transcription	Aorta	Aorta
20	chr16:12272800-12281600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr16:12275400-12280800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr16:12276600-12279600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr16:12276600-12281600	Weak transcription	Brain Germinal Matrix	brain
24	chr16:12276800-12296800	Weak transcription	Gastric	stomach
25	chr16:12277400-12279800	Strong transcription	Primary T cells from cord blood	blood
26	chr16:12277600-12286400	Strong transcription	Primary B cells from cord blood	blood
27	chr16:12277800-12279800	Enhancers	Placenta	Placenta
28	chr16:12278000-12284600	Enhancers	HSMMtube	muscle
29	chr16:12278200-12279800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr16:12278200-12281800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr16:12278400-12279800	Enhancers	HSMM	muscle
32	chr16:12278400-12280800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr16:12278600-12279800	Enhancers	Brain Anterior Caudate	brain
34	chr16:12278600-12283000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr16:12278600-12299400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr16:12278800-12279800	Enhancers	Brain Substantia Nigra	brain
37	chr16:12278800-12282600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr16:12279000-12279600	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr16:12279000-12279800	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr16:12279000-12280000	Enhancers	Fetal Muscle Leg	muscle
41	chr16:12279000-12280000	Enhancers	NHEK	skin
42	chr16:12279000-12282400	Weak transcription	Psoas Muscle	Psoas
43	chr16:12279000-12283600	Enhancers	Esophagus	oesophagus
44	chr16:12279200-12280400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr16:12279200-12282200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr16:12279400-12279800	Enhancers	Muscle Satellite Cultured Cells	--
47	chr16:12279400-12279800	Enhancers	Brain Hippocampus Middle	brain
48	chr16:12279400-12279800	Enhancers	Spleen	Spleen
49	chr16:12279400-12280800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr16:12279400-12281000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links