Variant report

Variant	rs1226594
Chromosome Location	chr9:103352968-103352969
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:103350659..103353280-chr9:103360412..103361939,2	K562	blood:
2	chr9:103189259..103191094-chr9:103351193..103354003,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066697	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10819773	0.80[YRI][hapmap]
rs10819776	0.82[YRI][hapmap]
rs10819789	0.82[YRI][hapmap]
rs10989082	0.85[YRI][hapmap]
rs10989094	0.82[YRI][hapmap]
rs10989168	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1135455	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226588	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]
rs1226592	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1226596	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[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	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2151597	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2183990	0.82[YRI][hapmap]
rs2183991	0.82[YRI][hapmap]
rs2489363	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2489364	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2780954	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2780958	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2800283	0.80[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2800288	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2800289	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7031884	0.82[YRI][hapmap]
rs72735191	0.97[ASN][1000 genomes]
rs951868	0.83[ASW][hapmap];0.80[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv893624	chr9:103351931-103416553	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1226594	GRIN3A	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103329600-103360800	Weak transcription	Aorta	Aorta
2	chr9:103330000-103357800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:103331600-103360200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr9:103332400-103357600	Weak transcription	Fetal Lung	lung
5	chr9:103333600-103360800	Weak transcription	Fetal Brain Male	brain
6	chr9:103343200-103360600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:103346200-103359800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:103346600-103353600	Weak transcription	Psoas Muscle	Psoas
9	chr9:103348400-103353400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:103348600-103361000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:103348800-103360600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:103349000-103353200	Enhancers	HUVEC	blood vessel
13	chr9:103349200-103353000	Weak transcription	Brain Anterior Caudate	brain
14	chr9:103349600-103360800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:103349800-103359400	Weak transcription	Brain Germinal Matrix	brain
16	chr9:103350000-103353200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr9:103350000-103353600	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:103350000-103357600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:103350000-103357600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr9:103350000-103360200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr9:103350200-103357600	Weak transcription	Fetal Brain Female	brain
22	chr9:103350200-103360200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:103350400-103357600	Weak transcription	Hela-S3	cervix
24	chr9:103350400-103359200	Weak transcription	Fetal Heart	heart
25	chr9:103350400-103360000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr9:103350600-103360800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr9:103350800-103357600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr9:103351000-103360000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr9:103351000-103360600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:103351200-103357600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr9:103351400-103353600	Enhancers	NHDF-Ad	bronchial
32	chr9:103351400-103354200	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr9:103351400-103354400	Enhancers	Brain Hippocampus Middle	brain
34	chr9:103351600-103353800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:103351600-103355600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:103351600-103360600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:103351800-103353400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:103351800-103353600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:103351800-103353800	Enhancers	Osteobl	bone
40	chr9:103351800-103354000	Enhancers	HSMMtube	muscle
41	chr9:103351800-103354400	Enhancers	Brain Substantia Nigra	brain
42	chr9:103352000-103353400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:103352000-103353600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr9:103352000-103353800	Enhancers	NHLF	lung
45	chr9:103352000-103354000	Enhancers	HSMM	muscle
46	chr9:103352000-103354800	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr9:103352200-103353200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr9:103352200-103353400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:103352200-103353800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr9:103352200-103354200	Enhancers	Brain Angular Gyrus	brain

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