Variant report

Variant	rs388887
Chromosome Location	chr5:16658524-16658525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:16657520..16659492-chr5:16660163..16661678,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12652580	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12658355	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13177228	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2247349	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2434517	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2560837	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2561234	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2561861	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2592041	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2592042	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2637153	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs371028	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs371805	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs373575	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs377309	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs378330	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs379803	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs381709	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs387793	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs398985	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs403174	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs407524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs410112	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs411918	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs415694	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs422821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs423247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs423465	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs428263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429234	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs434347	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs438138	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs439102	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs446224	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs447220	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs447562	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs447746	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs454031	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs588367	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs598302	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs664262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667563	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs676018	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs676852	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs685875	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs876095	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]

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	esv13219	chr5:16650304-16660144	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv869660	chr5:16651289-16766428	Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv597308	chr5:16655375-16658524	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs388887	MARCH11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16650000-16664600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr5:16652600-16663000	Weak transcription	Primary T cells from cord blood	blood
3	chr5:16653800-16663600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:16655800-16664000	Weak transcription	Pancreas	Pancrea
5	chr5:16655800-16670600	Weak transcription	Esophagus	oesophagus
6	chr5:16657000-16664000	Weak transcription	Fetal Brain Female	brain
7	chr5:16657000-16665600	Weak transcription	Osteobl	bone
8	chr5:16657000-16668000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:16657200-16660400	Weak transcription	Placenta	Placenta
10	chr5:16657200-16662800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:16657200-16663800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:16657200-16663800	Weak transcription	HMEC	breast
13	chr5:16657400-16663200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:16657400-16664000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr5:16657400-16665600	Weak transcription	NHDF-Ad	bronchial
16	chr5:16657600-16658800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:16657800-16666600	Weak transcription	Adipose Nuclei	Adipose
18	chr5:16658000-16663800	Weak transcription	NHEK	skin
19	chr5:16658200-16670400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:16658400-16663600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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