Variant report

Variant	rs11583836
Chromosome Location	chr1:85696534-85696535
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85694538..85697394-chr1:85706640..85709318,2	MCF-7	breast:
2	chr1:85665411..85671906-chr1:85683759..85698338,27	MCF-7	breast:
3	chr1:85669385..85672155-chr1:85695196..85696982,2	MCF-7	breast:
4	chr1:85574832..85575806-chr1:85695994..85696897,7	MCF-7	breast:
5	chr1:85694772..85696982-chr1:85723069..85725397,2	MCF-7	breast:
6	chr1:85574839..85575735-chr1:85696191..85696800,2	K562	blood:
7	chr1:85665829..85668570-chr1:85695074..85696808,2	K562	blood:

Variant related genes	Relation type
ENSG00000097096	Chromatin interaction
ENSG00000162642	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10493762	0.83[JPT][hapmap]
rs11161556	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161574	0.88[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11161584	0.86[EUR][1000 genomes]
rs11577656	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12563295	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17122364	0.84[JPT][hapmap]
rs17123650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17590006	1.00[YRI][hapmap]
rs2054238	0.83[JPT][hapmap]
rs2252408	0.91[EUR][1000 genomes]
rs2647396	0.89[JPT][hapmap]
rs2735587	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2735591	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2735592	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2735593	0.83[CEU][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes]
rs2735594	0.83[CEU][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes]
rs36006436	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768226	1.00[YRI][hapmap]
rs4255398	0.82[EUR][1000 genomes]
rs4907139	0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs4949892	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4949926	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60156243	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6663690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6671589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6693365	0.89[EUR][1000 genomes]
rs709790	0.80[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs72722613	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72722616	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72722624	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72722631	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72722638	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72722641	0.99[ASN][1000 genomes]
rs72722643	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7366220	0.83[EUR][1000 genomes];0.81[ASN][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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11583836	C1orf52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85687000-85709600	Weak transcription	Aorta	Aorta
2	chr1:85691800-85697000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:85692000-85697400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:85692200-85697400	Weak transcription	NHEK	skin
5	chr1:85694600-85696600	Enhancers	Stomach Mucosa	stomach
6	chr1:85695400-85696600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:85695600-85696600	Enhancers	Left Ventricle	heart
8	chr1:85696000-85696600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:85696000-85696600	Enhancers	H9 Cell Line	embryonic stem cell
10	chr1:85696000-85696600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:85696000-85696600	Enhancers	Adipose Nuclei	Adipose
12	chr1:85696200-85696600	Enhancers	Right Ventricle	heart
13	chr1:85696400-85696600	Enhancers	Right Atrium	heart
14	chr1:85696400-85705600	Weak transcription	Fetal Heart	heart

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