Variant report

Variant	rs1938921
Chromosome Location	chr11:86353920-86353921
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86352364..86354456-chr11:86522479..86524729,2	MCF-7	breast:
2	chr11:86346931..86348869-chr11:86351616..86354128,2	K562	blood:
3	chr11:86352044..86355103-chr11:86509980..86513018,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10792865	0.86[CHB][hapmap]
rs11234719	0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs11234731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11560984	0.80[AMR][1000 genomes]
rs12274942	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs12282010	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs12288119	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs17757676	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs1938929	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs1938931	0.93[ASN][1000 genomes]
rs1938932	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs1938935	1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs2017483	0.93[ASN][1000 genomes]
rs2155033	0.80[AMR][1000 genomes]
rs2212340	0.92[ASN][1000 genomes]
rs2212341	0.91[ASN][1000 genomes]
rs4144866	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4245417	0.93[ASN][1000 genomes]
rs4245418	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs4245419	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4245420	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4245421	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs4245422	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4245423	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4245424	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs4319536	0.86[CHB][hapmap]
rs4439535	0.93[ASN][1000 genomes]
rs4592448	0.86[CHB][hapmap]
rs4943948	0.88[ASN][1000 genomes]
rs4943949	0.93[ASN][1000 genomes]
rs4944602	0.93[ASN][1000 genomes]
rs4944603	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4944607	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4944609	0.93[ASN][1000 genomes]
rs4944611	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4944612	0.93[ASN][1000 genomes]
rs4944618	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4944620	0.80[AMR][1000 genomes]
rs496167	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs538058	0.81[CHB][hapmap]
rs550168	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs647782	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs656307	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6592301	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs6592302	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs661954	0.81[CHB][hapmap]
rs663543	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs670736	0.85[AMR][1000 genomes]
rs679220	0.81[CHB][hapmap]
rs7105863	1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs7106865	0.95[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs7115580	0.93[ASN][1000 genomes]
rs7115594	0.93[ASN][1000 genomes]
rs7115834	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs7120444	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs7123044	0.91[ASN][1000 genomes]
rs7937853	0.93[ASN][1000 genomes]
rs7938344	0.80[AMR][1000 genomes]
rs7941337	0.93[ASN][1000 genomes]
rs7941446	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs7948981	0.91[ASN][1000 genomes]
rs7951868	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs9787905	0.93[ASN][1000 genomes]
rs9943508	0.85[AMR][1000 genomes]
rs9943610	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs999472	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv555665	chr11:86230898-86417553	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1055071	chr11:86301240-86465465	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv555704	chr11:86344677-86386784	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1938921	ME3	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86340000-86357200	Weak transcription	Fetal Brain Female	brain
2	chr11:86341000-86355400	Weak transcription	Adipose Nuclei	Adipose
3	chr11:86341600-86358800	Weak transcription	Brain Anterior Caudate	brain
4	chr11:86342200-86356400	Weak transcription	Fetal Stomach	stomach
5	chr11:86344000-86373800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr11:86344600-86354600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr11:86344800-86355400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr11:86344800-86355800	Weak transcription	Pancreas	Pancrea
9	chr11:86346600-86359600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr11:86348800-86361600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:86349400-86356000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:86350600-86355000	Weak transcription	HMEC	breast
13	chr11:86350600-86355000	Weak transcription	NHLF	lung
14	chr11:86350600-86355200	Weak transcription	NH-A	brain
15	chr11:86350800-86354800	Weak transcription	NHDF-Ad	bronchial
16	chr11:86350800-86355200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:86350800-86355400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:86351000-86355000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:86351800-86354800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:86351800-86355800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:86352400-86355400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr11:86352600-86360600	Weak transcription	A549	lung
23	chr11:86353200-86354000	Enhancers	Aorta	Aorta
24	chr11:86353200-86355000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:86353200-86356200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:86353400-86354800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:86353400-86354800	Weak transcription	Osteobl	bone
28	chr11:86353400-86355200	Enhancers	Muscle Satellite Cultured Cells	--
29	chr11:86353400-86355400	Weak transcription	HSMM	muscle
30	chr11:86353600-86354000	Weak transcription	Ovary	ovary
31	chr11:86353600-86354400	Enhancers	Left Ventricle	heart
32	chr11:86353600-86354800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:86353600-86355000	Enhancers	Psoas Muscle	Psoas

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