Variant report

Variant	rs10277023
Chromosome Location	chr7:80709513-80709514
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10239474	0.86[EUR][1000 genomes]
rs10247169	0.80[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs10265624	0.91[EUR][1000 genomes]
rs10265745	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10267251	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10276120	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10277984	0.88[EUR][1000 genomes]
rs10480510	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10480511	0.87[CEU][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs10480852	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10480853	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12533994	0.94[ASN][1000 genomes]
rs12534374	0.81[JPT][hapmap]
rs12538655	0.86[EUR][1000 genomes]
rs12538859	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12540330	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12668893	0.90[EUR][1000 genomes]
rs13221460	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13240198	0.87[CEU][hapmap];0.83[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs1528736	0.86[EUR][1000 genomes]
rs17154740	0.93[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2247480	0.81[EUR][1000 genomes]
rs2247579	0.81[EUR][1000 genomes]
rs2697219	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697222	0.93[EUR][1000 genomes]
rs2697224	0.81[JPT][hapmap]
rs2697225	0.81[JPT][hapmap];0.81[TSI][hapmap]
rs2697943	0.80[CEU][hapmap];0.93[EUR][1000 genomes]
rs2697944	0.93[EUR][1000 genomes]
rs2697945	0.93[EUR][1000 genomes]
rs2697946	0.93[EUR][1000 genomes]
rs28715268	0.92[EUR][1000 genomes]
rs34344876	0.86[EUR][1000 genomes]
rs35876610	0.86[EUR][1000 genomes]
rs4540349	0.80[EUR][1000 genomes]
rs4573183	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4732106	0.87[EUR][1000 genomes]
rs61059308	0.86[EUR][1000 genomes]
rs62465327	0.90[ASN][1000 genomes]
rs6467539	0.86[JPT][hapmap];0.89[AFR][1000 genomes]
rs6467574	0.85[EUR][1000 genomes]
rs6944056	0.86[JPT][hapmap]
rs6955164	0.81[JPT][hapmap];0.81[TSI][hapmap]
rs6957232	0.81[TSI][hapmap]
rs71555084	0.89[AFR][1000 genomes]
rs7790887	0.92[EUR][1000 genomes]
rs7806015	0.86[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs949733	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv888524	chr7:80107798-80723062	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1034690	chr7:80520004-80987682	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv888551	chr7:80620397-80723062	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv888552	chr7:80683308-80755310	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv888553	chr7:80683308-80766407	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv888554	chr7:80695828-80755310	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv888555	chr7:80695828-80766407	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv888556	chr7:80695828-80797794	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	esv3333049	chr7:80709448-80709869	Enhancers	n/a	n/a	inside rSNPs	diseases
10	esv3508876	chr7:80709462-80709842	Enhancers	n/a	n/a	inside rSNPs	diseases
11	esv3508877	chr7:80709462-80709842	Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10277023	SEMA3C	cis	parietal	SCAN
rs10277023	RPL13AP17	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:80709200-80709600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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