Variant report

Variant	rs10104368
Chromosome Location	chr8:52680933-52680934
allele	A/C
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:78)

rs_ID	r²[population]
rs10086504	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10096943	0.86[JPT][hapmap]
rs10097328	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10110304	0.81[JPT][hapmap]
rs1022317	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs10504127	0.92[ASN][1000 genomes]
rs10504128	0.86[JPT][hapmap]
rs10504132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs1059041	0.86[JPT][hapmap]
rs1078888	0.86[JPT][hapmap]
rs10958299	0.86[JPT][hapmap]
rs11775601	0.86[JPT][hapmap]
rs11777885	0.94[JPT][hapmap]
rs11784921	0.88[JPT][hapmap]
rs12678479	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs13250860	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs13257067	0.86[JPT][hapmap]
rs13257291	0.86[JPT][hapmap]
rs13261243	0.86[JPT][hapmap]
rs13275235	0.86[JPT][hapmap]
rs13281179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1517305	0.86[JPT][hapmap]
rs16916800	0.92[ASN][1000 genomes]
rs16916878	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs16916903	0.82[ASN][1000 genomes]
rs16919843	0.92[ASN][1000 genomes]
rs2020431	0.82[ASN][1000 genomes]
rs2395857	0.86[JPT][hapmap]
rs28635761	1.00[ASN][1000 genomes]
rs28652885	1.00[ASN][1000 genomes]
rs3763547	0.81[GIH][hapmap];0.81[JPT][hapmap]
rs3824266	0.86[JPT][hapmap]
rs4259408	0.86[JPT][hapmap]
rs4294173	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs4324911	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs4330683	0.86[JPT][hapmap]
rs4361755	0.86[JPT][hapmap]
rs4570148	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs4584139	0.86[JPT][hapmap]
rs4587320	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs4596648	0.86[JPT][hapmap]
rs4612332	0.86[JPT][hapmap]
rs4618684	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs4634632	0.86[JPT][hapmap]
rs4873602	0.98[ASN][1000 genomes]
rs4873608	0.86[JPT][hapmap]
rs4873609	0.86[ASN][1000 genomes]
rs4873613	0.86[JPT][hapmap]
rs5002416	0.81[GIH][hapmap];0.82[JPT][hapmap]
rs58408501	0.98[ASN][1000 genomes]
rs58591247	0.94[ASN][1000 genomes]
rs59344101	0.97[ASN][1000 genomes]
rs7008057	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs7008721	1.00[ASN][1000 genomes]
rs7010217	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7011046	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7013587	0.86[JPT][hapmap]
rs7014075	0.86[JPT][hapmap]
rs7017450	0.86[JPT][hapmap]
rs73590413	1.00[ASN][1000 genomes]
rs73592226	0.82[ASN][1000 genomes]
rs7460311	0.86[JPT][hapmap]
rs7463120	0.86[JPT][hapmap]
rs7464192	0.86[JPT][hapmap]
rs7465225	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs753540	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs7829408	0.86[JPT][hapmap]
rs882492	0.86[JPT][hapmap]
rs884580	0.86[JPT][hapmap]
rs925763	0.86[JPT][hapmap]
rs9298463	0.85[JPT][hapmap]
rs9298464	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs9298466	0.86[JPT][hapmap]
rs9298467	0.81[JPT][hapmap]
rs950687	0.86[JPT][hapmap]
rs9643466	0.86[JPT][hapmap]
rs9643792	0.86[JPT][hapmap]
rs9643793	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	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
rs10104368	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52661400-52683200	Weak transcription	Left Ventricle	heart
2	chr8:52671800-52681800	Weak transcription	Right Atrium	heart
3	chr8:52676200-52682600	Weak transcription	Right Ventricle	heart
4	chr8:52680800-52681600	Weak transcription	GM12878-XiMat	blood

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