Variant report

Variant	rs10986948
Chromosome Location	chr9:101362101-101362102
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1034160	0.83[GIH][hapmap];0.86[TSI][hapmap]
rs10819071	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.98[LWK][hapmap];0.92[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10819072	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819074	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10986946	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1999500	0.86[TSI][hapmap]
rs2184025	0.81[GIH][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831665	chr9:101170061-101367692	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv893614	chr9:101340316-101671634	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv614950	chr9:101345778-101362833	Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv466440	chr9:101355624-101368008	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv614951	chr9:101355624-101368008	Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv893615	chr9:101356515-101678036	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10986948	IARS2	trans	cerebellum	SCAN
rs10986948	GRIN3A	cis	cerebellum	SCAN
rs10986948	CTSL2	cis	cerebellum	SCAN
rs10986948	BAAT	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101351600-101365800	Weak transcription	Right Atrium	heart
2	chr9:101356400-101363000	Weak transcription	Brain Angular Gyrus	brain
3	chr9:101359800-101365000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr9:101360000-101362200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:101360000-101362600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:101361800-101363400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:101362000-101362600	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr9:101362000-101363200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:101362000-101363200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:101362000-101363200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
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