Variant report

Variant	rs10912542
Chromosome Location	chr1:171167157-171167158
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10157270	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10489230	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10798240	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10798252	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10798253	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798263	0.80[ASN][1000 genomes]
rs10912475	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912529	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10912537	0.81[ASN][1000 genomes]
rs10912538	0.81[ASN][1000 genomes]
rs10912552	0.80[ASN][1000 genomes]
rs11806072	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11810116	0.81[ASN][1000 genomes]
rs12069067	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12078953	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12080576	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12090485	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12133385	0.96[ASN][1000 genomes]
rs12405613	0.96[ASN][1000 genomes]
rs12566823	0.80[ASN][1000 genomes]
rs12567956	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12730305	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17350523	0.95[ASN][1000 genomes]
rs1989656	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2008706	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2020861	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2049922	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2064078	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2075987	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075990	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2075991	0.99[ASN][1000 genomes]
rs2179105	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2205723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205724	0.80[ASN][1000 genomes]
rs2205727	0.94[ASN][1000 genomes]
rs2205728	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2205729	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2223228	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2223232	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2236874	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2421709	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2421710	0.96[ASN][1000 genomes]
rs2421711	0.96[ASN][1000 genomes]
rs35152982	0.95[ASN][1000 genomes]
rs3738813	0.96[ASN][1000 genomes]
rs3754494	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3768570	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4480395	0.91[ASN][1000 genomes]
rs4916182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916191	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916192	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425394	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6425413	0.96[ASN][1000 genomes]
rs6657314	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6662773	0.81[ASN][1000 genomes]
rs6672029	0.94[ASN][1000 genomes]
rs6692260	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692347	0.81[ASN][1000 genomes]
rs6699803	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701076	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6703439	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7513485	0.96[ASN][1000 genomes]
rs7513579	0.81[ASN][1000 genomes]
rs7518899	0.81[ASN][1000 genomes]
rs7520777	0.93[ASN][1000 genomes]
rs7524635	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7525342	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7529080	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7531713	0.91[ASN][1000 genomes]
rs7531971	0.94[ASN][1000 genomes]
rs7536822	0.96[ASN][1000 genomes]
rs7538013	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7539549	0.80[ASN][1000 genomes]
rs7545923	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7553869	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7887505	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs926268	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10912542	RP1-127D3.4	cis	Artery Tibial	GTEx
rs10912542	FMO2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171156600-171169800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr1:171156600-171177200	Weak transcription	Esophagus	oesophagus
3	chr1:171156600-171179600	Weak transcription	NHLF	lung
4	chr1:171156800-171179600	Weak transcription	Right Ventricle	heart
5	chr1:171161000-171171800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:171163000-171167400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:171163600-171167200	Enhancers	Fetal Intestine Large	intestine
8	chr1:171165400-171168800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:171165600-171167400	Enhancers	Ovary	ovary
10	chr1:171165600-171173400	Strong transcription	Left Ventricle	heart
11	chr1:171165800-171174400	Weak transcription	Stomach Mucosa	stomach
12	chr1:171166000-171169600	Strong transcription	Aorta	Aorta
13	chr1:171166000-171174600	Weak transcription	Pancreas	Pancrea
14	chr1:171166000-171178000	Weak transcription	Psoas Muscle	Psoas
15	chr1:171166000-171184000	Weak transcription	Gastric	stomach
16	chr1:171166400-171169400	Weak transcription	Right Atrium	heart
17	chr1:171166600-171168400	Weak transcription	Lung	lung
18	chr1:171166600-171175400	Strong transcription	Adipose Nuclei	Adipose
19	chr1:171166800-171167200	Active TSS	Fetal Brain Male	brain
20	chr1:171166800-171167400	Enhancers	Fetal Lung	lung
21	chr1:171167000-171167200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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