Variant report

Variant	rs4147306
Chromosome Location	chr8:52876352-52876353
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:52860243..52863481-chr8:52874076..52876433,3	MCF-7	breast:
2	chr8:52870845..52873668-chr8:52875256..52877463,2	K562	blood:

Variant related genes	Relation type
ENSG00000272024	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12550430	0.83[ASN][1000 genomes]
rs1996260	0.91[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs2090259	0.83[ASN][1000 genomes]
rs2090260	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2102727	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4873622	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4873624	0.82[ASN][1000 genomes]
rs4873625	0.82[ASN][1000 genomes]
rs4873626	0.83[ASN][1000 genomes]
rs4873627	0.83[ASN][1000 genomes]
rs4873628	0.83[ASN][1000 genomes]
rs4873629	0.83[ASN][1000 genomes]
rs4873630	0.83[ASN][1000 genomes]
rs4873631	0.83[ASN][1000 genomes]
rs4873632	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs55996614	0.83[ASN][1000 genomes]
rs57711556	0.83[ASN][1000 genomes]
rs6473670	0.91[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs6473671	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6473672	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6982231	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6987076	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6993367	0.81[ASW][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs7004360	0.83[ASN][1000 genomes]
rs7820670	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4147306	PCMTD1	cis	cerebellum	SCAN
rs4147306	SMAD4	trans	parietal	SCAN
rs4147306	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52874200-52876600	Enhancers	Placenta Amnion	Placenta Amnion
2	chr8:52874600-52876400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr8:52875200-52876600	Enhancers	Gastric	stomach
4	chr8:52875400-52876400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:52875400-52876600	Enhancers	Primary T cells fromperipheralblood	blood
6	chr8:52875400-52876600	Enhancers	Fetal Muscle Leg	muscle
7	chr8:52875400-52876600	Enhancers	Right Ventricle	heart
8	chr8:52875400-52876800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr8:52875400-52884800	Weak transcription	Pancreas	Pancrea
10	chr8:52875600-52876400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr8:52875600-52876600	Enhancers	Primary T cells from cord blood	blood
12	chr8:52875600-52876600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr8:52875600-52876600	Enhancers	Fetal Lung	lung
14	chr8:52875600-52876600	Enhancers	Psoas Muscle	Psoas
15	chr8:52875600-52876800	Enhancers	Colon Smooth Muscle	Colon
16	chr8:52875600-52876800	Enhancers	Fetal Heart	heart
17	chr8:52875600-52876800	Enhancers	Stomach Mucosa	stomach
18	chr8:52875800-52876400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr8:52875800-52876400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr8:52875800-52876400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr8:52875800-52876400	Enhancers	Primary hematopoietic stem cells	blood
22	chr8:52875800-52876400	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr8:52875800-52876400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr8:52875800-52876400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr8:52875800-52876600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr8:52875800-52876600	Enhancers	Right Atrium	heart
27	chr8:52875800-52876600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr8:52875800-52876600	Enhancers	Stomach Smooth Muscle	stomach
29	chr8:52875800-52876800	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr8:52875800-52876800	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr8:52875800-52876800	Enhancers	GM12878-XiMat	blood
32	chr8:52875800-52876800	Enhancers	HSMMtube	muscle
33	chr8:52875800-52877000	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr8:52875800-52877000	Enhancers	HepG2	liver
35	chr8:52875800-52886200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr8:52876000-52876600	Weak transcription	Fetal Intestine Small	intestine
37	chr8:52876200-52876600	Enhancers	Small Intestine	intestine
38	chr8:52876200-52877400	Weak transcription	HSMM	muscle

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