Variant report

Variant	rs3861706
Chromosome Location	chr9:14947472-14947473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10810294	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10810295	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10810296	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10810297	0.96[ASN][1000 genomes]
rs10810298	0.96[ASN][1000 genomes]
rs10810299	0.95[ASN][1000 genomes]
rs10810305	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10810306	0.86[ASN][1000 genomes]
rs10810307	0.88[ASN][1000 genomes]
rs10810308	0.88[ASN][1000 genomes]
rs10810309	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10810310	0.96[CEU][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10810311	0.81[AMR][1000 genomes]
rs10810312	0.81[AMR][1000 genomes]
rs10961792	0.81[EUR][1000 genomes]
rs10961806	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10961809	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10961814	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10961817	0.87[ASN][1000 genomes]
rs10961819	0.81[JPT][hapmap]
rs11515200	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11515203	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11793253	0.97[ASN][1000 genomes]
rs12335682	0.81[AMR][1000 genomes]
rs12340301	0.88[ASN][1000 genomes]
rs12378196	0.94[ASN][1000 genomes]
rs12379705	0.91[ASN][1000 genomes]
rs1357474	0.94[ASN][1000 genomes]
rs1403560	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1589666	0.96[ASN][1000 genomes]
rs1829850	0.95[ASN][1000 genomes]
rs1880013	0.87[ASN][1000 genomes]
rs2049291	0.95[ASN][1000 genomes]
rs2049292	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2381973	0.97[ASN][1000 genomes]
rs4546746	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4553007	0.81[JPT][hapmap]
rs62536769	0.80[AMR][1000 genomes]
rs7020107	0.87[ASN][1000 genomes]
rs7028104	0.81[JPT][hapmap]
rs7028135	0.97[ASN][1000 genomes]
rs7042782	0.97[ASN][1000 genomes]
rs7043477	0.88[ASN][1000 genomes]
rs7048509	0.81[JPT][hapmap]
rs7350286	0.91[ASN][1000 genomes]
rs7350287	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv613637	chr9:14524438-15011915	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv831518	chr9:14760638-14953501	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv613647	chr9:14852141-15016475	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv892620	chr9:14922877-15086021	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv892621	chr9:14928013-15043692	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3861706	RP11-54D18.2	cis	Nerve Tibial	GTEx
rs3861706	RP11-54D18.2	cis	Muscle Skeletal	GTEx
rs3861706	RP11-54D18.2	cis	Esophagus Muscularis	GTEx
rs3861706	RP11-54D18.2	cis	Artery Aorta	GTEx
rs3861706	RP11-54D18.2	cis	Thyroid	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14933200-14957200	Weak transcription	Fetal Muscle Leg	muscle
2	chr9:14942000-14950200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:14942400-14949400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr9:14942800-14949600	Weak transcription	Fetal Stomach	stomach
5	chr9:14945800-14949400	Weak transcription	Placenta	Placenta
6	chr9:14947200-14947600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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