Variant report

Variant	rs17821897
Chromosome Location	chr16:12660850-12660851
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12656706..12658781-chr16:12659071..12661791,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11639553	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11640455	0.83[AMR][1000 genomes]
rs11640862	0.85[CEU][hapmap]
rs11642881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11643010	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11643162	0.86[AMR][1000 genomes]
rs11644221	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11645658	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11646569	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11646611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11647633	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11648724	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12148951	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12149441	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12325256	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17223249	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17223442	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.95[AMR][1000 genomes]
rs2042915	0.81[ASN][1000 genomes]
rs34147303	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3803606	0.85[CEU][hapmap]
rs4780457	0.88[ASN][1000 genomes]
rs55645382	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55779146	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55910004	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56013945	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62028253	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62028254	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62028663	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62028664	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62028744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62028746	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62028749	0.92[AMR][1000 genomes]
rs62029200	0.83[AMR][1000 genomes]
rs7190533	0.81[EUR][1000 genomes]
rs7191878	0.81[EUR][1000 genomes]
rs7197122	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7198815	0.92[CEU][hapmap]
rs7198944	0.92[CEU][hapmap]
rs72775274	0.88[ASN][1000 genomes]
rs72775290	0.85[AMR][1000 genomes]
rs8053336	0.92[CEU][hapmap]
rs9452	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9926489	0.85[AMR][1000 genomes]
rs9926499	0.85[AMR][1000 genomes]
rs9936658	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1051242	chr16:12482972-12897243	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv542749	chr16:12482972-12897243	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1035581	chr16:12516946-12863700	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1051607	chr16:12522130-13347676	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv542750	chr16:12522130-13347676	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	esv1842867	chr16:12632286-12678721	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv2751546	chr16:12635498-12674704	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1050925	chr16:12648058-12670588	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1044772	chr16:12648266-12668751	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1049011	chr16:12655176-12672143	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv9349	chr16:12656022-12674639	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17821897	GRIN2A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12613000-12670800	Weak transcription	Pancreas	Pancrea
2	chr16:12632800-12663800	Weak transcription	Aorta	Aorta
3	chr16:12641200-12667000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr16:12642000-12662200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr16:12645200-12661600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr16:12646000-12661000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr16:12647400-12662200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr16:12647400-12665200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr16:12647600-12661600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr16:12648000-12662200	Weak transcription	Fetal Stomach	stomach
11	chr16:12648400-12668800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr16:12649800-12662200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr16:12652200-12669200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr16:12652400-12666400	Weak transcription	Brain Anterior Caudate	brain
15	chr16:12652600-12665800	Weak transcription	Brain Angular Gyrus	brain
16	chr16:12652600-12672200	Weak transcription	Right Ventricle	heart
17	chr16:12652800-12663400	Weak transcription	Brain Substantia Nigra	brain
18	chr16:12653200-12662200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr16:12653200-12667600	Weak transcription	Brain Hippocampus Middle	brain
20	chr16:12653200-12669200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr16:12653600-12662400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr16:12653600-12662600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr16:12653600-12663200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr16:12653800-12662600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr16:12653800-12665800	Weak transcription	NHDF-Ad	bronchial
26	chr16:12656000-12661600	Weak transcription	Spleen	Spleen
27	chr16:12656000-12662200	Weak transcription	Gastric	stomach
28	chr16:12656400-12664200	Weak transcription	Left Ventricle	heart
29	chr16:12657600-12664400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr16:12659000-12661800	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr16:12659200-12662200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr16:12659400-12662000	Enhancers	Primary T cells fromperipheralblood	blood
33	chr16:12659600-12662200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr16:12659600-12662200	Weak transcription	Esophagus	oesophagus
35	chr16:12659600-12663200	Weak transcription	Placenta	Placenta
36	chr16:12659600-12664000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr16:12659600-12666000	Strong transcription	Primary B cells from peripheral blood	blood
38	chr16:12659800-12661400	Enhancers	Ovary	ovary
39	chr16:12659800-12661800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr16:12659800-12662400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr16:12659800-12663400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr16:12660000-12661800	Enhancers	Primary T cells from cord blood	blood
43	chr16:12660000-12662000	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr16:12660000-12666200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr16:12660200-12661000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr16:12660200-12661000	Enhancers	HepG2	liver
47	chr16:12660200-12661800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr16:12660200-12663000	Weak transcription	GM12878-XiMat	blood
49	chr16:12660200-12663400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr16:12660400-12661000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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