Variant report

Variant	rs56055736
Chromosome Location	chr9:86531858-86531859
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	chr9:86531254..86532896-chr9:86534357..86536311,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10868069	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10868072	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11140284	0.82[AMR][1000 genomes]
rs11999592	0.84[AMR][1000 genomes]
rs12001293	0.80[EUR][1000 genomes]
rs12001505	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12001918	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12003101	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12003500	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12552069	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086750	0.87[EUR][1000 genomes]
rs2184086	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2990915	0.82[EUR][1000 genomes]
rs34690696	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35784768	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4480186	0.92[EUR][1000 genomes]
rs55654273	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55872219	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57267691	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57531526	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57957686	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58248061	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58474042	0.98[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs60277614	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61490202	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62561948	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7036293	0.84[AMR][1000 genomes]
rs7038235	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7040843	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7041687	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7042053	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7046229	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048626	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73463313	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73463327	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73463379	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73463395	0.98[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs73469343	0.91[EUR][1000 genomes]
rs7849708	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7850288	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7850404	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7850640	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7854432	0.98[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7857619	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859830	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859928	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7864058	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7874481	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9695726	0.93[AMR][1000 genomes]
rs970846	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv8541	chr9:86469723-86593758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv438108	chr9:86488586-86542206	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56055736	C4orf31	trans	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86461600-86535400	Weak transcription	Fetal Intestine Small	intestine
2	chr9:86461600-86535400	Weak transcription	Ovary	ovary
3	chr9:86462200-86535200	Weak transcription	Fetal Brain Female	brain
4	chr9:86462600-86535200	Weak transcription	Brain Anterior Caudate	brain
5	chr9:86481000-86535800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr9:86491000-86535200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:86491200-86535200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:86496000-86535000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:86496400-86533000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:86499400-86535000	Weak transcription	Fetal Kidney	kidney
11	chr9:86500000-86534800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr9:86500200-86535200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:86500200-86535200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr9:86500200-86535600	Weak transcription	Lung	lung
15	chr9:86502000-86532400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:86502600-86535000	Weak transcription	Fetal Lung	lung
17	chr9:86506400-86534800	Weak transcription	Pancreas	Pancrea
18	chr9:86508200-86535600	Weak transcription	Esophagus	oesophagus
19	chr9:86512400-86535400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr9:86512600-86535400	Weak transcription	Placenta	Placenta
21	chr9:86513200-86534800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:86516200-86535000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:86517400-86535200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr9:86517600-86535000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr9:86518800-86535000	Weak transcription	Primary B cells from cord blood	blood
26	chr9:86518800-86535000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr9:86518800-86535200	Weak transcription	Thymus	Thymus
28	chr9:86519000-86535000	Weak transcription	Fetal Muscle Leg	muscle
29	chr9:86519000-86535400	Weak transcription	Fetal Stomach	stomach
30	chr9:86520000-86533000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr9:86520400-86535400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr9:86523800-86535000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr9:86523800-86535000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr9:86525000-86535000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr9:86525600-86535000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:86525600-86535600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:86525600-86535600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:86526400-86535200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:86527200-86535000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:86528600-86535000	Weak transcription	Fetal Intestine Large	intestine
41	chr9:86531200-86535000	Weak transcription	NHEK	skin
42	chr9:86531600-86535200	Weak transcription	Osteobl	bone
43	chr9:86531600-86535400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:86531800-86535200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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