Variant report

Variant	rs10156478
Chromosome Location	chr9:103875396-103875397
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10989391	1.00[MKK][hapmap]
rs12342841	0.90[MEX][hapmap]
rs12344631	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12345440	0.90[MEX][hapmap]
rs12351067	0.86[MEX][hapmap]
rs12352151	0.90[MEX][hapmap]
rs12685239	0.90[MEX][hapmap]
rs1410854	0.81[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1431477	0.90[MEX][hapmap]
rs61342570	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67133619	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7029916	0.90[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428542	chr9:103709079-103878127	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv831669	chr9:103709125-103878122	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv831671	chr9:103858107-104020816	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10156478	LPPR1	cis	cerebellum	SCAN
rs10156478	NR4A3	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103870800-103876600	Weak transcription	Brain Anterior Caudate	brain
2	chr9:103874200-103875400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:103874200-103877200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr9:103874400-103877000	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr9:103874600-103875400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr9:103874600-103878000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr9:103874800-103878000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr9:103875000-103875400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr9:103875000-103875400	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr9:103875000-103876200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr9:103875200-103876000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:103875200-103876200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:103875200-103876200	Weak transcription	Brain Hippocampus Middle	brain
14	chr9:103875200-103876400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr9:103875200-103876600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:103875200-103876600	Weak transcription	Fetal Brain Female	brain

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

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