Variant report

Variant	rs1226588
Chromosome Location	chr9:103341014-103341015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10819776	0.85[YRI][hapmap]
rs10819782	0.82[YRI][hapmap]
rs10819785	0.82[YRI][hapmap]
rs10819789	0.85[YRI][hapmap]
rs10989082	0.82[YRI][hapmap]
rs10989094	0.85[YRI][hapmap]
rs10989097	0.81[YRI][hapmap]
rs10989168	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1135455	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793014	0.82[YRI][hapmap]
rs1226592	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1226594	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226596	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13291670	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13301089	0.97[ASN][1000 genomes]
rs1760290	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1930246	0.82[YRI][hapmap]
rs2151597	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2183990	0.85[YRI][hapmap]
rs2183991	0.85[YRI][hapmap]
rs2489363	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2489364	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2780954	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2780958	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2800283	0.80[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2800288	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2800289	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7028822	0.82[YRI][hapmap]
rs72735191	0.97[ASN][1000 genomes]
rs951868	0.80[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1226588	GRIN3A	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103307400-103341800	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr9:103307400-103347800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:103308600-103345400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:103311800-103342400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:103318400-103342400	Weak transcription	Brain Anterior Caudate	brain
6	chr9:103318600-103344000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:103322600-103341800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:103323400-103342000	Weak transcription	Brain Angular Gyrus	brain
9	chr9:103324800-103345400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:103327800-103349400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:103329600-103360800	Weak transcription	Aorta	Aorta
12	chr9:103329800-103351800	Weak transcription	Ovary	ovary
13	chr9:103330000-103357800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr9:103330400-103345400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:103330400-103351600	Weak transcription	Fetal Stomach	stomach
16	chr9:103330800-103349400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr9:103331600-103360200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:103332400-103351600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:103332400-103357600	Weak transcription	Fetal Lung	lung
20	chr9:103333600-103360800	Weak transcription	Fetal Brain Male	brain
21	chr9:103334200-103341200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:103334200-103351000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:103334600-103350600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:103334800-103350200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:103335000-103351000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr9:103335400-103341400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr9:103335600-103341200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:103336800-103347800	Weak transcription	Brain Germinal Matrix	brain
29	chr9:103337400-103342800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:103337600-103352200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr9:103338600-103348000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr9:103338800-103352200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr9:103339600-103341200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:103339600-103344600	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr9:103340000-103342600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr9:103340000-103344400	Active TSS	HSMMtube	muscle
37	chr9:103340000-103344600	Active TSS	Fetal Muscle Leg	muscle
38	chr9:103340000-103344600	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr9:103340200-103341200	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:103340200-103341200	Enhancers	Brain Hippocampus Middle	brain
41	chr9:103340200-103341200	Active TSS	Left Ventricle	heart
42	chr9:103340200-103341200	Active TSS	Psoas Muscle	Psoas
43	chr9:103340200-103342200	Weak transcription	NH-A	brain
44	chr9:103340200-103344200	Active TSS	Right Atrium	heart
45	chr9:103340200-103344400	Active TSS	Right Ventricle	heart
46	chr9:103340200-103344800	Active TSS	Fetal Muscle Trunk	muscle
47	chr9:103340400-103341200	Enhancers	Brain Substantia Nigra	brain
48	chr9:103340400-103342200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:103340400-103344000	Active TSS	Fetal Heart	heart
50	chr9:103340600-103342000	Weak transcription	NHLF	lung

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