Variant report

Variant	rs3983746
Chromosome Location	chr9:103877068-103877069
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10119316	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1019873	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10512278	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10989419	0.89[GIH][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs12352148	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1367754	1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1431478	1.00[JPT][hapmap]
rs17761685	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17762396	1.00[CEU][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs17829436	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs17829926	1.00[CEU][hapmap];0.82[GIH][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs1987400	1.00[CEU][hapmap]
rs41274975	0.85[ASN][1000 genomes]
rs4278208	1.00[CEU][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs4742806	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs4743445	1.00[CEU][hapmap];0.82[GIH][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs4743449	1.00[CEU][hapmap]
rs4743450	1.00[CEU][hapmap]
rs58422308	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60195477	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60390009	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61647398	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66858224	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72741426	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72741430	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72741431	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72741444	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7852006	1.00[CEU][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
rs3983746	C9orf125	cis	parietal	SCAN
rs3983746	C9orf156	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103874200-103877200	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr9:103874600-103878000	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr9:103874800-103878000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr9:103875800-103878200	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr9:103876000-103877600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:103876200-103877400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr9:103876200-103877600	Enhancers	H9 Cell Line	embryonic stem cell
8	chr9:103876200-103877800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr9:103876200-103878400	Enhancers	Brain Hippocampus Middle	brain
10	chr9:103876400-103877600	Enhancers	H1 Cell Line	embryonic stem cell
11	chr9:103876400-103877600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:103876400-103879600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr9:103876600-103877200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr9:103876600-103877600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr9:103876600-103877800	Enhancers	HUVEC	blood vessel
16	chr9:103876600-103878000	Enhancers	Fetal Brain Female	brain
17	chr9:103876600-103878200	Enhancers	Brain Anterior Caudate	brain
18	chr9:103876800-103877600	Enhancers	Fetal Brain Male	brain
19	chr9:103877000-103877400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr9:103877000-103877800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr9:103877000-103877800	Enhancers	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links