Variant report

Variant	rs2538975
Chromosome Location	chr7:147586474-147586475
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11980029	0.94[ASW][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12533758	0.81[JPT][hapmap]
rs12536467	0.84[CHB][hapmap]
rs12539201	0.84[CHB][hapmap]
rs2011815	0.84[CHB][hapmap]
rs2215798	0.94[ASW][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2538964	0.81[YRI][hapmap]
rs2538973	0.81[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2538976	0.89[LWK][hapmap]
rs2708242	0.94[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2708244	0.94[ASW][hapmap];0.98[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs2708259	0.86[AFR][1000 genomes]
rs2710101	0.84[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2710103	1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2710106	0.86[AFR][1000 genomes]
rs2710109	0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap]
rs35814206	0.88[ASN][1000 genomes]
rs57921419	0.88[ASN][1000 genomes]
rs60467763	0.88[ASN][1000 genomes]
rs60967951	0.88[ASN][1000 genomes]

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	nsv1023913	chr7:147521075-147806318	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1026058	chr7:147521109-147783042	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv539179	chr7:147521109-147783042	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv934002	chr7:147521110-147807705	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1017610	chr7:147523752-147806427	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv889398	chr7:147569595-147588768	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a
7	nsv608966	chr7:147574479-147588768	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	n/a
8	esv3441359	chr7:147585772-147592059	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2538975	ZNF398	cis	cerebellum	SCAN
rs2538975	SSPO	cis	parietal	SCAN
rs2538975	NKX3-2	trans	parietal	SCAN
rs2538975	ABCB8	cis	cerebellum	SCAN
rs2538975	ACTR3C	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:147582000-147589400	Weak transcription	Brain Substantia Nigra	brain

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