Variant report

Variant	rs9818684
Chromosome Location	chr3:156524220-156524221
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:156521817..156525806-chr3:156525939..156530007,4	MCF-7	breast:
2	chr3:156523470..156525861-chr3:156534229..156535791,2	MCF-7	breast:
3	chr3:156388866..156397270-chr3:156524172..156537549,71	MCF-7	breast:
4	chr3:156522791..156525819-chr3:156530782..156532939,3	MCF-7	breast:
5	chr3:156511086..156512603-chr3:156522561..156524791,2	MCF-7	breast:
6	chr3:156517201..156520390-chr3:156522150..156525155,3	K562	blood:
7	chr3:156515560..156517669-chr3:156523840..156525586,2	K562	blood:
8	chr3:156424358..156426182-chr3:156523815..156525710,2	MCF-7	breast:
9	chr3:156401467..156404144-chr3:156522121..156524308,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-6F2.7.1-3	chr3:156522228-156525596	NONHSAT092867

No data

Variant related genes	Relation type
ENSG00000230457	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000240875	Chromatin interaction
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10212230	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs10936037	0.81[EUR][1000 genomes]
rs10936038	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10936040	0.89[CEU][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs10936043	0.85[CEU][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs11707914	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11711674	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11717133	0.81[AMR][1000 genomes]
rs12107178	0.82[ASN][1000 genomes]
rs12492804	0.81[AMR][1000 genomes]
rs12492968	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629380	0.81[EUR][1000 genomes]
rs12634915	0.89[CEU][hapmap];0.80[JPT][hapmap];0.86[TSI][hapmap]
rs12638253	0.85[CEU][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs13068223	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs13086516	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13088978	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs13097325	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13322318	0.89[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs1384538	0.85[CEU][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs1430410	0.89[TSI][hapmap];0.81[AMR][1000 genomes]
rs1430411	0.81[AMR][1000 genomes]
rs1560415	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1560416	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17382070	0.82[EUR][1000 genomes]
rs1835372	0.81[AMR][1000 genomes]
rs1995425	0.80[JPT][hapmap]
rs2054880	0.82[CHB][hapmap]
rs2060015	0.83[EUR][1000 genomes]
rs2321290	0.89[CEU][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs2321292	0.89[CEU][hapmap];0.80[JPT][hapmap];0.88[YRI][hapmap]
rs2321455	0.80[JPT][hapmap]
rs2874494	0.92[CEU][hapmap];0.89[YRI][hapmap]
rs2874495	0.80[JPT][hapmap]
rs343994	0.82[CHB][hapmap]
rs34667021	0.81[EUR][1000 genomes]
rs3851992	0.83[CHD][hapmap]
rs3910072	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4098	0.92[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4680305	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4680312	0.88[CEU][hapmap];0.80[JPT][hapmap]
rs4680317	0.93[ASW][hapmap];0.89[CEU][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs59717073	0.81[AMR][1000 genomes]
rs6780427	0.89[CEU][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs6803064	0.80[JPT][hapmap]
rs7615304	0.81[GIH][hapmap];0.80[JPT][hapmap]
rs7623691	0.88[ASN][1000 genomes]
rs7637701	0.85[CEU][hapmap];0.80[JPT][hapmap]
rs7638625	0.93[ASW][hapmap];0.85[CEU][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9812169	0.81[AMR][1000 genomes]
rs9812895	0.82[EUR][1000 genomes]
rs9814813	0.81[GIH][hapmap]
rs9818780	0.87[ASN][1000 genomes]
rs9820830	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9837038	0.85[CEU][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs9837271	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9842198	0.81[AMR][1000 genomes]
rs9844054	0.89[CEU][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs9847187	0.89[CEU][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs9858861	0.84[TSI][hapmap];0.81[AMR][1000 genomes]
rs9859058	0.90[ASN][1000 genomes]
rs9865905	0.85[CEU][hapmap];0.80[JPT][hapmap]
rs9867621	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs9867857	0.85[ASN][1000 genomes]
rs9871817	0.85[ASW][hapmap];0.89[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs9876010	0.89[CEU][hapmap];0.83[GIH][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs987724	0.81[GIH][hapmap];0.80[JPT][hapmap]
rs9878566	0.87[ASN][1000 genomes]
rs9878585	0.89[CEU][hapmap];0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9818684	LINC00886	cis	Thyroid	GTEx
rs9818684	LINC00886	cis	Adipose Subcutaneous	GTEx
rs9818684	LINC00886	cis	Artery Aorta	GTEx
rs9818684	PPM1L	cis	cerebellum	SCAN
rs9818684	LINC00886	cis	Muscle Skeletal	GTEx
rs9818684	SNORA5C	trans	cerebellum	SCAN
rs9818684	LINC00886	cis	Stomach	GTEx
rs9818684	LINC00886	cis	Nerve Tibial	GTEx
rs9818684	LINC00886	cis	Esophagus Muscularis	GTEx
rs9818684	LINC00886	cis	Esophagus Mucosa	GTEx
rs9818684	LINC00886	cis	Artery Tibial	GTEx
rs9818684	LINC00886	cis	lung	GTEx
rs9818684	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156502800-156528400	Weak transcription	Esophagus	oesophagus
2	chr3:156502800-156529000	Weak transcription	Liver	Liver
3	chr3:156511200-156529000	Weak transcription	Primary T cells from cord blood	blood
4	chr3:156511400-156530400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:156514400-156525400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:156514400-156525800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:156517400-156529000	Weak transcription	A549	lung
8	chr3:156518000-156524800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:156518000-156529800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:156520200-156525800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:156520200-156530400	Weak transcription	Right Ventricle	heart
12	chr3:156520400-156524800	Weak transcription	NHEK	skin
13	chr3:156520400-156525800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:156522200-156525800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:156522200-156526000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:156522200-156530400	Weak transcription	Gastric	stomach
17	chr3:156522400-156529000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:156523000-156525000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:156523000-156526600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:156523400-156527400	Weak transcription	GM12878-XiMat	blood
21	chr3:156524000-156526600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:156524000-156527200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:156524200-156525000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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