Variant report

Variant	rs11980029
Chromosome Location	chr7:147583680-147583681
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11561915	0.93[JPT][hapmap]
rs11561916	0.93[JPT][hapmap]
rs11769191	0.81[CEU][hapmap]
rs11771110	1.00[CEU][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12533758	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12540934	0.83[CHB][hapmap]
rs13223313	0.85[JPT][hapmap]
rs13225365	0.85[JPT][hapmap]
rs13233606	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs13234998	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs13235220	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs17237331	0.93[JPT][hapmap]
rs1861009	0.93[JPT][hapmap]
rs2215798	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2538964	0.81[YRI][hapmap]
rs2538973	1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2538975	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]
rs2538976	0.86[LWK][hapmap]
rs2708242	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708244	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2708259	0.85[AFR][1000 genomes]
rs2710101	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2710103	0.81[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2710106	0.85[AFR][1000 genomes]
rs2710109	0.98[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs35814206	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57921419	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60467763	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60967951	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6946545	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7805083	0.91[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889397	chr7:147471710-147585819	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
2	nsv465193	chr7:147512619-147583680	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
3	nsv608965	chr7:147512619-147583680	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
4	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
5	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
6	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
7	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
8	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
9	nsv889398	chr7:147569595-147588768	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a
10	nsv608966	chr7:147574479-147588768	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11980029	ACTR3C	cis	parietal	SCAN
rs11980029	ACCN3	cis	cerebellum	SCAN
rs11980029	ZNF398	cis	cerebellum	SCAN
rs11980029	SSPO	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:147582000-147584000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr7:147582000-147589400	Weak transcription	Brain Substantia Nigra	brain

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