Variant report

Variant	rs1704130
Chromosome Location	chr16:12297987-12297988
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12292330..12294859-chr16:12296467..12299466,2	MCF-7	breast:
2	chr16:12292359..12294226-chr16:12296818..12299210,2	K562	blood:

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

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

rs_ID	r²[population]
rs11642667	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1701111	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1704094	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2456272	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2968353	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs709418	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs709419	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs709420	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs709421	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs709422	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8062913	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs830696	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs830698	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs830700	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs830701	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs830704	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs830705	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs830706	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs830707	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs830708	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs830709	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs830710	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs830724	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs830725	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844224	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs844225	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853869	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs853870	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs862692	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs865533	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs866180	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs905952	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937965	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9934120	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[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
rs1704130	GRIN2A	cis	parietal	SCAN

Chromatin state (count:63 , 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	chr16:12261800-12322000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr16:12278600-12299400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:12282800-12298800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr16:12282800-12305400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr16:12282800-12322600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr16:12283000-12298200	Weak transcription	Left Ventricle	heart
8	chr16:12283200-12298200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr16:12283200-12300200	Weak transcription	NHEK	skin
10	chr16:12283200-12302000	Weak transcription	NHDF-Ad	bronchial
11	chr16:12283400-12310200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr16:12287200-12299200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr16:12287800-12302200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr16:12290800-12299200	Weak transcription	Esophagus	oesophagus
15	chr16:12291400-12316200	Strong transcription	Primary T cells from cord blood	blood
16	chr16:12292200-12322200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr16:12292600-12300400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr16:12292600-12301400	Weak transcription	GM12878-XiMat	blood
19	chr16:12292800-12310200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr16:12293000-12302400	Strong transcription	Primary B cells from cord blood	blood
21	chr16:12293200-12300200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr16:12293600-12319800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr16:12294200-12299800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr16:12294800-12298400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr16:12294800-12298600	Weak transcription	Aorta	Aorta
26	chr16:12294800-12322400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr16:12295000-12298600	Weak transcription	Adipose Nuclei	Adipose
28	chr16:12295200-12311400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr16:12295400-12298200	Enhancers	Placenta	Placenta
30	chr16:12295600-12319800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr16:12295800-12320800	Weak transcription	HSMMtube	muscle
32	chr16:12296000-12298600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr16:12296200-12319800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr16:12296400-12299600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr16:12296600-12298200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr16:12296600-12299600	Genic enhancers	Spleen	Spleen
37	chr16:12296600-12322600	Weak transcription	Right Ventricle	heart
38	chr16:12296800-12313000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr16:12297000-12298400	Enhancers	Brain Substantia Nigra	brain
40	chr16:12297000-12299400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr16:12297000-12301400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr16:12297000-12301800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr16:12297000-12322400	Weak transcription	Ovary	ovary
44	chr16:12297200-12298800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr16:12297200-12299400	Weak transcription	Lung	lung
46	chr16:12297200-12305000	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr16:12297200-12305800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr16:12297200-12309600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr16:12297400-12298200	Enhancers	Fetal Muscle Leg	muscle
50	chr16:12297400-12298600	Weak transcription	Fetal Muscle Trunk	muscle

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