Variant report

Variant	rs2184025
Chromosome Location	chr9:101359237-101359238
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1034160	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10819071	0.83[GIH][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs10819072	0.81[GIH][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs10819073	0.81[EUR][1000 genomes]
rs10986946	0.81[EUR][1000 genomes]
rs10986948	0.81[GIH][hapmap];0.86[TSI][hapmap]
rs1999499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1999500	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2778909	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs2778910	0.81[CEU][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs870047	0.83[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv466438	chr9:101328200-101361584	Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv614949	chr9:101328200-101361584	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	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
6	nsv614950	chr9:101345778-101362833	Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	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
8	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
9	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2184025	LPPR1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101351600-101365800	Weak transcription	Right Atrium	heart
2	chr9:101356400-101362000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:101356400-101363000	Weak transcription	Brain Angular Gyrus	brain
4	chr9:101356600-101360000	Enhancers	Fetal Brain Male	brain
5	chr9:101358000-101360000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:101358800-101359800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:101358800-101360000	Enhancers	Fetal Brain Female	brain
8	chr9:101359000-101359400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr9:101359000-101359400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:101359000-101359400	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr9:101359000-101360000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:101359000-101360000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr9:101359200-101359400	Enhancers	HUES6 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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