Variant report

Variant	rs2237565
Chromosome Location	chr7:86455536-86455537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10085604	0.84[ASN][1000 genomes]
rs1468412	0.84[ASN][1000 genomes]
rs17126	0.86[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs2237562	0.84[ASN][1000 genomes]
rs2237566	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282966	0.86[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs6465088	0.93[ASW][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6944519	0.97[ASN][1000 genomes]
rs6944719	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6977175	0.84[ASN][1000 genomes]
rs7804907	0.84[ASN][1000 genomes]
rs7806785	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025032	chr7:86032479-86642973	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv532147	chr7:86299225-87121975	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2237565	GRM3	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86442200-86468400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr7:86443400-86480600	Weak transcription	Brain Angular Gyrus	brain
3	chr7:86453400-86455800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:86453400-86468400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:86454400-86455800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:86454600-86456000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr7:86454600-86456000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr7:86454600-86456400	Enhancers	Brain Substantia Nigra	brain
9	chr7:86454800-86455800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:86454800-86455800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr7:86454800-86455800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr7:86454800-86456000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:86454800-86456000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr7:86454800-86456400	Enhancers	Brain Anterior Caudate	brain
15	chr7:86454800-86456400	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr7:86455000-86456000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr7:86455000-86456200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:86455200-86456600	Enhancers	Brain Hippocampus Middle	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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