Variant report

Variant	rs60277614
Chromosome Location	chr9:86498454-86498455
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10868069	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10868072	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11140284	0.82[AMR][1000 genomes]
rs11999592	0.84[AMR][1000 genomes]
rs12001505	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12001918	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12003101	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12003500	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12552069	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17086750	0.86[EUR][1000 genomes]
rs2184086	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2990915	0.85[EUR][1000 genomes]
rs34690696	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35784768	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480186	0.89[EUR][1000 genomes]
rs55654273	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55872219	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56045327	0.82[ASN][1000 genomes]
rs56055736	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57267691	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57531526	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57957686	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58248061	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58474042	0.90[EUR][1000 genomes]
rs61490202	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62561948	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7036293	0.84[AMR][1000 genomes]
rs7038235	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7040843	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041687	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7042053	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7046229	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7048626	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73463313	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73463327	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73463379	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73463395	0.90[EUR][1000 genomes]
rs73469343	0.88[EUR][1000 genomes]
rs7849708	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7850288	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7850404	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7850640	0.89[EUR][1000 genomes]
rs7854432	0.89[EUR][1000 genomes]
rs7857619	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7859830	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7859928	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7864058	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7874481	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9695726	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs970846	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[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
rs60277614	C4orf31	trans	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86460600-86518200	Weak transcription	Thymus	Thymus
2	chr9:86461600-86535400	Weak transcription	Fetal Intestine Small	intestine
3	chr9:86461600-86535400	Weak transcription	Ovary	ovary
4	chr9:86462200-86535200	Weak transcription	Fetal Brain Female	brain
5	chr9:86462600-86499200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr9:86462600-86500600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:86462600-86503800	Weak transcription	Dnd41	blood
8	chr9:86462600-86535200	Weak transcription	Brain Anterior Caudate	brain
9	chr9:86462800-86515000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:86462800-86518000	Weak transcription	Fetal Intestine Large	intestine
11	chr9:86462800-86518000	Weak transcription	Fetal Stomach	stomach
12	chr9:86481000-86535800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr9:86482000-86518000	Weak transcription	Left Ventricle	heart
14	chr9:86490400-86510800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:86491000-86535200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr9:86491200-86502200	Weak transcription	Brain Germinal Matrix	brain
17	chr9:86491200-86535200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr9:86491400-86518000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:86491800-86518200	Weak transcription	Primary B cells from cord blood	blood
20	chr9:86492000-86500600	Weak transcription	Fetal Lung	lung
21	chr9:86493600-86500000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:86495000-86518000	Weak transcription	Primary T cells from cord blood	blood
23	chr9:86496000-86535000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:86496400-86500400	Weak transcription	Hela-S3	cervix
25	chr9:86496400-86533000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:86496600-86515600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr9:86497600-86499800	Weak transcription	HMEC	breast
28	chr9:86497800-86500200	Weak transcription	NHEK	skin

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