Variant report

Variant	rs12678680
Chromosome Location	chr8:52668449-52668450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10504130	1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs10958300	0.83[AMR][1000 genomes]
rs10958301	0.83[AMR][1000 genomes]
rs10958305	1.00[YRI][hapmap]
rs11775587	1.00[YRI][hapmap]
rs11775611	1.00[YRI][hapmap]
rs11777016	0.83[AMR][1000 genomes]
rs11777714	0.83[AMR][1000 genomes]
rs11778164	0.82[ASN][1000 genomes]
rs11778849	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11780891	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11781330	0.84[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs11785467	0.82[ASN][1000 genomes]
rs11785805	1.00[YRI][hapmap]
rs11786167	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12674620	0.94[ASN][1000 genomes]
rs12675786	0.88[AMR][1000 genomes]
rs12675907	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12678646	1.00[ASN][1000 genomes]
rs13274159	0.82[ASN][1000 genomes]
rs13275967	0.82[ASN][1000 genomes]
rs16916820	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16916856	0.88[AMR][1000 genomes]
rs16916865	1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs16916906	0.83[AMR][1000 genomes]
rs17284746	1.00[YRI][hapmap]
rs34004633	0.82[ASN][1000 genomes]
rs34067888	0.82[ASN][1000 genomes]
rs34780436	0.82[ASN][1000 genomes]
rs34973406	0.85[AMR][1000 genomes]
rs41453644	1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs4418329	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4421347	0.82[ASN][1000 genomes]
rs4425745	0.82[ASN][1000 genomes]
rs4436115	0.82[ASN][1000 genomes]
rs4442134	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4554456	0.83[ASN][1000 genomes]
rs4573262	0.82[ASN][1000 genomes]
rs4626584	0.82[ASN][1000 genomes]
rs4873592	0.82[ASN][1000 genomes]
rs57212480	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58561048	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58583070	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61326367	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6473653	0.97[ASN][1000 genomes]
rs6473654	0.87[ASN][1000 genomes]
rs6768	1.00[YRI][hapmap]
rs6994203	1.00[YRI][hapmap]
rs7001968	0.83[ASN][1000 genomes]
rs71513544	0.82[ASN][1000 genomes]
rs71513546	0.94[ASN][1000 genomes]
rs7459977	0.82[ASN][1000 genomes]
rs763550	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932026	chr8:51858658-52758574	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv890898	chr8:52579964-52680933	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv831316	chr8:52660353-52842928	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12678680	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52661400-52671400	Weak transcription	Right Atrium	heart
2	chr8:52661400-52683200	Weak transcription	Left Ventricle	heart
3	chr8:52666400-52675800	Weak transcription	Right Ventricle	heart

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