Variant report

Variant	rs2512987
Chromosome Location	chr11:86414282-86414283
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86411235..86420303-chr11:86507153..86518645,29	MCF-7	breast:
2	chr11:86378621..86386201-chr11:86413884..86420246,14	MCF-7	breast:
3	chr11:86414005..86419352-chr11:86508550..86514510,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151376	Chromatin interaction
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1938936	0.95[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs2433420	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2433421	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2508304	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2512981	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2512982	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2512984	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2512985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2512986	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2512988	0.95[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs507211	0.82[CHB][hapmap]
rs642245	0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv428263	chr11:86357990-86508480	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1049157	chr11:86409059-86504155	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Adverse response to chemotherapy (neutropenia/leucopenia) (doxorubicin)	23648065	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2512987	C11orf82	cis	parietal	SCAN
rs2512987	CTSC	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86386600-86431000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:86399600-86415800	Weak transcription	Fetal Heart	heart
3	chr11:86400600-86414800	Weak transcription	Ovary	ovary
4	chr11:86407000-86451600	Weak transcription	Left Ventricle	heart
5	chr11:86407600-86417000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr11:86408000-86431400	Weak transcription	Aorta	Aorta
7	chr11:86410600-86419800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr11:86410800-86416400	Weak transcription	A549	lung
9	chr11:86410800-86419400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:86410800-86420200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:86411000-86428000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:86411000-86429000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr11:86412400-86418800	Enhancers	Colon Smooth Muscle	Colon
14	chr11:86412600-86414400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr11:86412800-86414600	Enhancers	Rectal Smooth Muscle	rectum
16	chr11:86413600-86415800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:86413800-86416200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr11:86414000-86416600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr11:86414000-86418000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr11:86414200-86415600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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