Variant report

Variant	rs848912
Chromosome Location	chr7:78998409-78998410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10231862	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10240210	0.80[EUR][1000 genomes]
rs10256590	0.86[EUR][1000 genomes]
rs10269174	0.84[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs10953840	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17152303	0.82[JPT][hapmap]
rs17421752	0.84[EUR][1000 genomes]
rs2190178	0.81[EUR][1000 genomes]
rs2364916	0.84[EUR][1000 genomes]
rs28427380	0.84[EUR][1000 genomes]
rs4260838	0.92[EUR][1000 genomes]
rs4730769	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6950887	0.84[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs704865	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7804560	0.82[JPT][hapmap]
rs848904	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848905	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848906	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848907	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs848908	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs848918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs848919	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs848920	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs848922	0.96[CEU][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848923	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848925	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848930	0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848936	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848937	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs848939	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs848942	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs848943	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs848949	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848952	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848954	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848955	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848956	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs860247	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9692383	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs991077	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs991260	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9969364	0.84[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]

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	nsv464598	chr7:78492642-79483480	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv607659	chr7:78492642-79483480	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1029799	chr7:78608097-79061737	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2764028	chr7:78874740-79112630	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv464600	chr7:78981719-79030922	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv607663	chr7:78981719-79030922	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv888513	chr7:78983840-79023504	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv888514	chr7:78987060-79061837	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv888515	chr7:78987060-79221707	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv607664	chr7:78998409-79057761	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs848912	TMEM120A	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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