Variant report

Variant	rs754694
Chromosome Location	chr3:136752551-136752552
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs108858	0.88[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13095028	0.83[CEU][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap]
rs13095034	0.86[EUR][1000 genomes]
rs1385306	0.90[EUR][1000 genomes]
rs1470142	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1654900	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1654901	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1682361	0.88[EUR][1000 genomes]
rs1682362	0.89[EUR][1000 genomes]
rs1682363	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1682364	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1682365	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1682366	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs181732	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2086880	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2117008	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2344092	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34564994	0.86[EUR][1000 genomes]
rs361227	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs361228	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs361229	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs361231	0.86[EUR][1000 genomes]
rs361232	0.88[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs361233	0.88[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs361234	0.87[EUR][1000 genomes]
rs361235	0.88[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.87[EUR][1000 genomes]
rs4678278	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4678281	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55781515	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6439677	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6439678	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6766766	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766858	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802479	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640951	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7646307	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835627	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs835628	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs835629	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs835630	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs835631	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs835651	0.84[EUR][1000 genomes]
rs835652	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs900947	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs900948	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs900949	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs900950	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9681468	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9817061	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9827066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845076	0.84[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.85[EUR][1000 genomes]
rs9850024	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9854795	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9874615	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs999038	0.84[AMR][1000 genomes];0.91[EUR][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	nsv877534	chr3:136676303-136765859	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv524856	chr3:136693459-137190765	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1012111	chr3:136695367-137343430	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv4028	chr3:136752048-136777353	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs754694	ACPL2	cis	parietal	SCAN
rs754694	SPSB4	cis	cerebellum	SCAN
rs754694	PCCB	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136745800-136755000	Weak transcription	NHEK	skin
2	chr3:136748000-136754800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:136751600-136752600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:136752000-136752600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:136752000-136752600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:136752000-136756600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:136752000-136764600	Weak transcription	Esophagus	oesophagus
8	chr3:136752200-136752600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
9	chr3:136752200-136752600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:136752200-136752800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
11	chr3:136752200-136752800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
12	chr3:136752200-136752800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
13	chr3:136752200-136754400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:136752200-136754800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:136752400-136753000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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