Variant report

Variant	rs2968353
Chromosome Location	chr16:12293992-12293993
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	chr16:12292359..12294226-chr16:12296818..12299210,2	K562	blood:
2	chr16:12292330..12294859-chr16:12296467..12299466,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11642667	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1701111	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1704094	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1704130	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2456272	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs709418	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs709419	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs709420	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs709421	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs709422	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8062913	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs830696	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs830698	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs830700	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs830701	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs830704	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs830705	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs830706	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs830707	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs830708	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs830709	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs830710	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs830724	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs830725	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844224	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs844225	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853869	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs853870	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs862692	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs865533	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs866180	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs905952	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs937965	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9934120	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2968353	GRIN2A	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12242200-12299400	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr16:12257000-12296800	Weak transcription	Thymus	Thymus
3	chr16:12261800-12322000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr16:12276800-12296800	Weak transcription	Gastric	stomach
5	chr16:12278600-12299400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr16:12279800-12297800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr16:12281200-12297000	Weak transcription	Lung	lung
8	chr16:12282800-12297200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr16:12282800-12298800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr16:12282800-12305400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr16:12282800-12322600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr16:12283000-12296400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr16:12283000-12296600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr16:12283000-12298200	Weak transcription	Left Ventricle	heart
15	chr16:12283200-12298200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr16:12283200-12300200	Weak transcription	NHEK	skin
17	chr16:12283200-12302000	Weak transcription	NHDF-Ad	bronchial
18	chr16:12283400-12310200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr16:12284600-12295400	Weak transcription	HSMMtube	muscle
20	chr16:12284600-12296200	Weak transcription	Fetal Muscle Leg	muscle
21	chr16:12284600-12296600	Weak transcription	Spleen	Spleen
22	chr16:12284800-12297800	Weak transcription	Fetal Thymus	thymus
23	chr16:12287200-12299200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr16:12287600-12294800	Weak transcription	Osteobl	bone
25	chr16:12287800-12294800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr16:12287800-12302200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr16:12288000-12296400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr16:12289600-12296200	Weak transcription	Fetal Stomach	stomach
29	chr16:12290800-12299200	Weak transcription	Esophagus	oesophagus
30	chr16:12291000-12294600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr16:12291000-12295400	Weak transcription	Placenta	Placenta
32	chr16:12291400-12316200	Strong transcription	Primary T cells from cord blood	blood
33	chr16:12292000-12295000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr16:12292200-12297000	Weak transcription	Brain Substantia Nigra	brain
35	chr16:12292200-12297200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr16:12292200-12297400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr16:12292200-12297600	Weak transcription	Brain Anterior Caudate	brain
38	chr16:12292200-12322200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr16:12292600-12297400	Weak transcription	Brain Hippocampus Middle	brain
40	chr16:12292600-12297600	Weak transcription	Brain Angular Gyrus	brain
41	chr16:12292600-12297600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr16:12292600-12300400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr16:12292600-12301400	Weak transcription	GM12878-XiMat	blood
44	chr16:12292800-12310200	Strong transcription	Primary B cells from peripheral blood	blood
45	chr16:12293000-12294400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr16:12293000-12297000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr16:12293000-12302400	Strong transcription	Primary B cells from cord blood	blood
48	chr16:12293200-12300200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr16:12293400-12294000	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr16:12293400-12294000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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