Variant report

Variant	rs11778849
Chromosome Location	chr8:52708254-52708255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10087958	0.82[JPT][hapmap]
rs10504130	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[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10958300	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10958301	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10958305	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs11775587	0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs11775611	0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs11777016	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11777714	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11780040	0.98[ASN][1000 genomes]
rs11780891	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11781330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11784869	0.94[ASN][1000 genomes]
rs11785805	0.92[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs11786167	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11787229	0.86[ASN][1000 genomes]
rs12675786	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12675907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12676345	0.89[ASN][1000 genomes]
rs12676780	0.93[ASN][1000 genomes]
rs12676835	0.94[ASN][1000 genomes]
rs12677407	0.94[ASN][1000 genomes]
rs12678639	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12678680	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12679287	0.94[ASN][1000 genomes]
rs12679983	0.88[ASN][1000 genomes]
rs12680128	0.88[ASN][1000 genomes]
rs12681203	0.94[ASN][1000 genomes]
rs12681734	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs13265006	0.98[ASN][1000 genomes]
rs13276400	0.89[ASN][1000 genomes]
rs16916820	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16916856	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16916865	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16916906	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16916961	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17212214	0.94[ASN][1000 genomes]
rs17212256	0.94[ASN][1000 genomes]
rs17284746	0.92[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs2037138	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2037139	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2069119	0.89[ASN][1000 genomes]
rs2176120	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34058697	0.95[ASN][1000 genomes]
rs34073804	0.90[ASN][1000 genomes]
rs34213209	0.89[ASN][1000 genomes]
rs34319820	0.90[ASN][1000 genomes]
rs34364864	1.00[ASN][1000 genomes]
rs34372756	0.94[ASN][1000 genomes]
rs34677273	0.94[ASN][1000 genomes]
rs34973406	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35032384	0.94[ASN][1000 genomes]
rs35509250	0.89[ASN][1000 genomes]
rs35603537	0.89[ASN][1000 genomes]
rs41453644	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[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4292674	0.88[ASN][1000 genomes]
rs4321994	0.87[ASN][1000 genomes]
rs4534123	0.88[ASN][1000 genomes]
rs4598243	0.96[ASN][1000 genomes]
rs4626585	0.88[ASN][1000 genomes]
rs57212480	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58561048	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58583070	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59602923	0.94[ASN][1000 genomes]
rs60153173	0.90[ASN][1000 genomes]
rs60304457	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60796336	0.94[ASN][1000 genomes]
rs61326367	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6768	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6994203	1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs71513549	0.88[ASN][1000 genomes]
rs71513552	0.90[ASN][1000 genomes]
rs71513561	0.98[ASN][1000 genomes]
rs71513564	0.94[ASN][1000 genomes]
rs763550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650179	0.94[ASN][1000 genomes]
rs9650180	0.94[ASN][1000 genomes]
rs9650305	0.94[ASN][1000 genomes]
rs9792352	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][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	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
6	nsv1023825	chr8:52668824-52716137	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11778849	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52704200-52712600	Weak transcription	Left Ventricle	heart
2	chr8:52705800-52716000	Weak transcription	Right Ventricle	heart
3	chr8:52708200-52708600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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