Variant report

Variant	rs7008730
Chromosome Location	chr8:52912977-52912978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12550430	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1996259	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1996260	0.85[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2090259	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2090260	0.87[ASN][1000 genomes]
rs2102727	0.87[ASN][1000 genomes]
rs4302862	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4873622	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4873624	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4873625	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4873626	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4873627	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4873628	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4873629	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4873630	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4873631	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4873632	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55996614	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57711556	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6473670	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6473671	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6473672	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6982231	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6983991	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6987717	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6992125	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6998696	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7003916	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7004360	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7008584	0.88[AFR][1000 genomes]
rs7012596	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7820670	0.86[ASN][1000 genomes]
rs964433	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	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
2	nsv1031672	chr8:52872448-52917469	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1020673	chr8:52878946-52917469	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1017700	chr8:52886765-52917469	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv520947	chr8:52887541-52915994	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv611353	chr8:52887541-52915994	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1027822	chr8:52897278-52916486	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7008730	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52912600-52913000	Enhancers	GM12878-XiMat	blood
2	chr8:52912600-52913400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr8:52912600-52913400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr8:52912600-52913400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr8:52912600-52913400	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr8:52912600-52913800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr8:52912600-52914400	Enhancers	Primary B cells from cord blood	blood
8	chr8:52912600-52914600	Enhancers	Primary B cells from peripheral blood	blood
9	chr8:52912800-52913000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
10	chr8:52912800-52913200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr8:52912800-52913200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr8:52912800-52913200	Enhancers	Fetal Thymus	thymus
13	chr8:52912800-52913200	Enhancers	HUVEC	blood vessel
14	chr8:52912800-52913400	Enhancers	Primary hematopoietic stem cells	blood
15	chr8:52912800-52913400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr8:52912800-52913400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr8:52912800-52913400	Enhancers	Spleen	Spleen
18	chr8:52912800-52913600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr8:52912800-52913600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr8:52912800-52913600	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr8:52912800-52913600	Enhancers	Dnd41	blood
22	chr8:52912800-52913800	Enhancers	Primary T cells from cord blood	blood
23	chr8:52912800-52913800	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr8:52912800-52913800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr8:52912800-52914000	Enhancers	Primary T helper cells fromperipheralblood	blood

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