Variant report

Variant	rs1829967
Chromosome Location	chr3:81940348-81940349
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1155277	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs11711331	0.85[GIH][hapmap]
rs11925940	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12495343	0.89[EUR][1000 genomes]
rs12635671	0.89[EUR][1000 genomes]
rs1404297	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1851917	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1971426	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1973800	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1973801	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1973803	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1973804	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1997002	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2030708	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2244294	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2252530	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2594547	1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs2594549	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs2594551	0.87[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs2594553	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs2594558	0.87[EUR][1000 genomes]
rs2594562	0.87[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2680245	1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs2680246	0.87[EUR][1000 genomes]
rs2680257	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs2680260	0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2680274	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2680277	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs2680280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691077	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2691078	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2691079	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2691080	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2691083	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2691085	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2691089	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691093	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs3772882	0.89[GIH][hapmap]
rs3772883	0.89[GIH][hapmap]
rs3821548	0.85[GIH][hapmap]
rs3849570	0.85[GIH][hapmap]
rs3860595	0.84[GIH][hapmap]
rs4273393	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4411908	0.89[GIH][hapmap]
rs4479621	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6774438	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6803932	1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs7611902	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620240	0.82[GIH][hapmap]
rs7653333	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs950904	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs957670	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9810377	0.81[EUR][1000 genomes]
rs9822266	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860204	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv999992	chr3:81693662-82015969	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv536605	chr3:81693662-82015969	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1829967	GRIN1	trans	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81938600-81940400	Weak transcription	Fetal Brain Female	brain
2	chr3:81938800-81940600	Weak transcription	Fetal Brain Male	brain
3	chr3:81939000-81940600	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr3:81939600-81940800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:81939600-81941200	Enhancers	H1 Cell Line	embryonic stem cell
6	chr3:81939600-81941200	Enhancers	Dnd41	blood
7	chr3:81939600-81942000	Enhancers	Fetal Thymus	thymus
8	chr3:81939800-81940400	Weak transcription	Psoas Muscle	Psoas
9	chr3:81940000-81941200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:81940000-81941400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr3:81940000-81941400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr3:81940200-81941000	Enhancers	H9 Cell Line	embryonic stem cell
13	chr3:81940200-81941000	Enhancers	Thymus	Thymus
14	chr3:81940200-81941200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:81940200-81941200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:81940200-81941200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr3:81940200-81941400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr3:81940200-81941400	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr3:81940200-81941400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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