Variant report

Variant	rs12712628
Chromosome Location	chr2:39113610-39113611
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr2:39113310-39113660	K562	blood:	n/a	n/a
2	NR2F2	chr2:39113212-39113706	K562	blood:	n/a	n/a

Variant related genes	Relation type
RNU6-851P	TF binding region
ARHGEF33	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1010858	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1010859	0.91[EUR][1000 genomes]
rs10181808	0.80[EUR][1000 genomes]
rs10204999	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11124651	0.89[AFR][1000 genomes]
rs11124654	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11124655	0.82[AMR][1000 genomes]
rs1131752	0.80[EUR][1000 genomes]
rs11675110	0.83[AFR][1000 genomes]
rs11689954	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12373604	0.91[AFR][1000 genomes]
rs12465365	0.86[AFR][1000 genomes]
rs12617734	0.86[AFR][1000 genomes]
rs12621073	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12712627	0.89[AFR][1000 genomes]
rs13029388	0.89[AFR][1000 genomes]
rs13035182	0.87[EUR][1000 genomes]
rs17422748	0.88[EUR][1000 genomes]
rs1901289	0.93[AFR][1000 genomes]
rs2060743	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3099940	0.81[EUR][1000 genomes]
rs3099941	0.81[EUR][1000 genomes]
rs3099942	0.84[EUR][1000 genomes]
rs3099958	0.93[EUR][1000 genomes]
rs3099959	0.89[EUR][1000 genomes]
rs3099998	0.81[EUR][1000 genomes]
rs373300	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs389023	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4133043	0.86[AFR][1000 genomes]
rs4641916	0.88[AFR][1000 genomes]
rs4670268	0.83[EUR][1000 genomes]
rs4670899	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6544180	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6706091	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6706186	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6710418	0.89[AFR][1000 genomes]
rs6732083	0.86[AFR][1000 genomes]
rs6738069	0.82[EUR][1000 genomes]
rs6738403	0.88[AFR][1000 genomes]
rs6744514	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6754902	0.86[EUR][1000 genomes]
rs7598922	0.91[AFR][1000 genomes]
rs9808136	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active 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 target site	143 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12712628	DHX57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39103800-39114000	Weak transcription	Lung	lung
2	chr2:39103800-39120200	Weak transcription	Left Ventricle	heart
3	chr2:39104000-39114200	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:39104200-39113800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:39104200-39113800	Weak transcription	Fetal Lung	lung
6	chr2:39104200-39114400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:39104200-39114400	Weak transcription	Colon Smooth Muscle	Colon
8	chr2:39104200-39114800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:39104200-39114800	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:39104200-39115800	Weak transcription	Brain Germinal Matrix	brain
11	chr2:39104200-39119400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:39104200-39122200	Weak transcription	Ovary	ovary
13	chr2:39104200-39129000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:39108400-39113800	Weak transcription	Brain Anterior Caudate	brain
15	chr2:39108800-39114600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:39110200-39186800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:39110400-39115800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:39110400-39120600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:39112800-39113800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr2:39113400-39113800	Enhancers	HSMMtube	muscle
21	chr2:39113600-39118800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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