Variant report

Variant	rs3105738
Chromosome Location	chr8:9889914-9889915
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10087802	0.90[JPT][hapmap]
rs10098342	1.00[JPT][hapmap]
rs10100022	0.90[JPT][hapmap]
rs10216752	1.00[JPT][hapmap]
rs11775290	0.87[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs11786541	0.82[CEU][hapmap]
rs11990555	0.90[JPT][hapmap]
rs11995711	0.93[ASN][1000 genomes]
rs12678797	0.80[CEU][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap]
rs12678800	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs13254175	0.80[CEU][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap]
rs13282106	0.80[CEU][hapmap]
rs1351876	0.80[CEU][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap]
rs1484639	0.80[CEU][hapmap]
rs1484640	0.80[CEU][hapmap]
rs1521194	0.90[ASN][1000 genomes]
rs17151071	1.00[JPT][hapmap]
rs17151244	0.90[JPT][hapmap]
rs17689674	0.84[CEU][hapmap]
rs2062331	0.80[CEU][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap]
rs2062332	0.89[JPT][hapmap]
rs4598253	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs483916	0.88[CEU][hapmap];0.83[GIH][hapmap]
rs4841282	0.90[JPT][hapmap]
rs525726	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs555200	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs643955	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647796	0.83[ASN][1000 genomes]
rs658385	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6601414	0.80[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs6601415	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs6983332	0.80[CEU][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap]
rs6986885	0.89[JPT][hapmap]
rs6986911	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs6995837	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs6995859	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs7823314	0.90[JPT][hapmap]
rs7823714	0.90[JPT][hapmap]
rs7832670	0.90[JPT][hapmap]
rs7833387	0.81[CEU][hapmap]
rs9329213	1.00[JPT][hapmap]
rs956824	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530864	chr8:9097498-9914548	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1023834	chr8:9798072-9904788	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916493	chr8:9806580-10029482	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv869934	chr8:9806639-9940586	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1034165	chr8:9821150-9906812	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv539465	chr8:9821150-9906812	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv890342	chr8:9864345-9897508	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv890343	chr8:9888729-9932797	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs3105738	MFHAS1	cis	cerebellum	SCAN
rs3105738	PPP1R3B	cis	lymphoblastoid	seeQTL
rs3105738	FLJ10661	cis	parietal	SCAN
rs3105738	DEFA6	cis	parietal	SCAN
rs3105738	FLJ10661	cis	cerebellum	SCAN
rs3105738	C8orf5	Cis_chr	lymphoblastoid	RTeQTL
rs3105738	CLDN23	cis	multi-tissue	Pritchard
rs3105738	TDH	cis	cerebellum	SCAN
rs3105738	PRSS55	cis	cerebellum	SCAN
rs3105738	DEFB134	cis	cerebellum	SCAN
rs3105738	DEFB136	cis	parietal	SCAN
rs3105738	CTSB	cis	cerebellum	SCAN
rs3105738	BLK	Cis_chr	lymphoblastoid	RTeQTL
rs3105738	C8orf13	cis	multi-tissue	Pritchard

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9887000-9892000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr8:9889200-9905400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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