Variant report

Variant	rs10898514
Chromosome Location	chr11:86331632-86331633
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:86330506..86332301-chr11:86511499..86514446,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10219173	0.96[ASN][1000 genomes]
rs10219305	0.97[ASN][1000 genomes]
rs10219319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10219378	0.98[ASN][1000 genomes]
rs10400291	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.94[ASN][1000 genomes]
rs10792860	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10792861	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10792862	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10792863	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10792864	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10792866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10898505	0.90[ASN][1000 genomes]
rs10898506	0.83[ASN][1000 genomes]
rs10898507	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10898510	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10898511	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10898512	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[MKK][hapmap];0.98[ASN][1000 genomes]
rs10898515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10898516	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11234717	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11535845	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12289252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12290684	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1540081	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1540082	0.88[CHB][hapmap];0.95[CHD][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs17211577	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1894012	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1938924	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1938925	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1938926	0.96[ASN][1000 genomes]
rs1938927	0.94[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[ASN][1000 genomes]
rs1938928	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1938938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2032356	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051433	0.85[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2155035	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2840368	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4144865	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4944601	0.88[ASN][1000 genomes]
rs4944604	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944613	0.94[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs722157	0.89[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes]
rs722158	0.89[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes]
rs7940587	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7940590	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7940772	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940788	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs949350	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9634021	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[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	nsv898057	chr11:86306401-86335459	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10898514	ME3	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86321800-86343200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:86322000-86334200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr11:86322000-86334200	Weak transcription	Left Ventricle	heart
4	chr11:86325000-86333000	Weak transcription	Stomach Mucosa	stomach
5	chr11:86329200-86331800	Weak transcription	Ovary	ovary
6	chr11:86329200-86333000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr11:86329200-86333000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr11:86330800-86332600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:86330800-86341600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:86331000-86343600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:86331000-86346200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr11:86331400-86332000	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr11:86331400-86332000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr11:86331400-86333000	Enhancers	Muscle Satellite Cultured Cells	--
15	chr11:86331400-86333200	Enhancers	Colon Smooth Muscle	Colon
16	chr11:86331400-86333200	Enhancers	Osteobl	bone
17	chr11:86331400-86333400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:86331400-86333400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr11:86331400-86333600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:86331600-86331800	Enhancers	Right Ventricle	heart
21	chr11:86331600-86332200	Enhancers	Fetal Muscle Leg	muscle
22	chr11:86331600-86332200	Enhancers	Right Atrium	heart
23	chr11:86331600-86332200	Enhancers	Stomach Smooth Muscle	stomach
24	chr11:86331600-86332600	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr11:86331600-86333200	Enhancers	Adipose Nuclei	Adipose
26	chr11:86331600-86333600	Enhancers	Fetal Stomach	stomach
27	chr11:86331600-86333800	Enhancers	NHDF-Ad	bronchial

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