Variant report

Variant	rs4870988
Chromosome Location	chr8:120884499-120884500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:120866641..120870729-chr8:120883446..120889946,10	MCF-7	breast:
2	chr8:120867684..120870037-chr8:120884451..120886345,2	K562	blood:
3	chr8:120883348..120885416-chr8:120993271..120996165,2	MCF-7	breast:
4	chr8:120876190..120878848-chr8:120883052..120885833,3	K562	blood:
5	chr8:120883686..120886465-chr8:121071792..121074526,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187955	Chromatin interaction
ENSG00000136982	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10094587	0.85[JPT][hapmap]
rs10103058	0.85[JPT][hapmap]
rs10107579	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10955941	0.85[JPT][hapmap]
rs10955943	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11781657	0.82[ASW][hapmap];0.85[JPT][hapmap]
rs11995536	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12548715	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12681402	0.85[JPT][hapmap]
rs12681623	0.82[ASW][hapmap];0.85[JPT][hapmap]
rs13257316	0.85[JPT][hapmap]
rs13260933	0.82[ASW][hapmap];0.85[JPT][hapmap]
rs13282901	0.85[JPT][hapmap]
rs1467044	0.85[JPT][hapmap]
rs16893258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984977	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2037346	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2326379	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28571066	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073560	0.85[JPT][hapmap]
rs4870986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4870991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871013	0.85[JPT][hapmap]
rs4871744	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871772	0.85[JPT][hapmap]
rs4871773	0.85[JPT][hapmap]
rs5022559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469861	0.85[JPT][hapmap]
rs6469863	0.85[JPT][hapmap]
rs6469867	0.85[JPT][hapmap]
rs6469868	0.85[JPT][hapmap]
rs6469871	0.85[JPT][hapmap]
rs6469872	0.85[JPT][hapmap]
rs6469878	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6980679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6981618	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6982701	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987580	0.82[ASW][hapmap];0.85[JPT][hapmap]
rs6988011	0.85[JPT][hapmap]
rs6995139	0.85[JPT][hapmap]
rs7000669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7002839	0.85[JPT][hapmap]
rs7005380	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7013639	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7018286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73703111	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73703112	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73703114	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73703115	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7387264	0.85[JPT][hapmap]
rs7387694	0.82[ASW][hapmap];0.85[JPT][hapmap]
rs7388508	0.85[JPT][hapmap]
rs7462250	0.85[JPT][hapmap]
rs7462302	0.82[ASW][hapmap];0.85[JPT][hapmap]
rs7465181	0.85[JPT][hapmap]
rs7814294	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7824545	0.85[JPT][hapmap]
rs7840156	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7840728	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs939241	0.85[JPT][hapmap]
rs955372	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9918814	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9918815	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9987332	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[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	nsv534028	chr8:120348940-120906079	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv949368	chr8:120568034-121019872	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1021071	chr8:120589963-120968317	Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv465789	chr8:120636850-120994394	Enhancers Strong transcription Weak transcription Flanking Active TSS 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	26 gene(s)	inside rSNPs	diseases
6	nsv612111	chr8:120636850-120994394	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv427826	chr8:120642181-120953395	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4870988	DEPDC6	cis	cerebellum	SCAN
rs4870988	ENPP2	cis	cerebellum	SCAN
rs4870988	ENPP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120868800-120885600	Weak transcription	Left Ventricle	heart
2	chr8:120869600-120885400	Weak transcription	Fetal Lung	lung
3	chr8:120875800-120885400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr8:120876000-120885200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr8:120876000-120885400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr8:120879400-120885400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr8:120879400-120885400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr8:120879400-120885400	Weak transcription	Brain Angular Gyrus	brain
9	chr8:120879600-120884600	Weak transcription	Colon Smooth Muscle	Colon
10	chr8:120879600-120885400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr8:120879600-120885400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr8:120879600-120885400	Weak transcription	A549	lung
13	chr8:120879600-120885600	Weak transcription	NHEK	skin
14	chr8:120879600-120885600	Weak transcription	NHLF	lung
15	chr8:120879800-120885000	Weak transcription	Liver	Liver
16	chr8:120879800-120885200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr8:120880000-120885400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr8:120882600-120884600	Enhancers	Hela-S3	cervix
19	chr8:120883000-120885600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr8:120883600-120885200	Weak transcription	Stomach Mucosa	stomach
21	chr8:120883600-120885400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr8:120883600-120885400	Weak transcription	HepG2	liver
23	chr8:120883600-120885400	Weak transcription	Osteobl	bone
24	chr8:120883600-120885600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr8:120883600-120885600	Weak transcription	Fetal Kidney	kidney
26	chr8:120883800-120885600	Weak transcription	HMEC	breast
27	chr8:120884000-120885400	Weak transcription	Brain Hippocampus Middle	brain
28	chr8:120884200-120885600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr8:120884400-120885400	Weak transcription	NH-A	brain

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