Variant report

Variant	rs540031
Chromosome Location	chr15:43608855-43608856
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43602565..43605136-chr15:43607378..43610157,2	K562	blood:
2	chr15:43608442..43611143-chr15:43626377..43627931,2	K562	blood:
3	chr15:43607344..43608879-chr15:43617306..43618965,2	MCF-7	breast:
4	chr15:43606779..43609028-chr15:43621318..43623726,3	MCF-7	breast:
5	chr15:43606648..43611125-chr15:43620820..43625585,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168803	Chromatin interaction
ENSG00000168806	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs1095386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070399	0.97[ASN][1000 genomes]
rs1123947	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1133395	0.97[ASN][1000 genomes]
rs11858152	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12101673	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12102205	0.97[ASN][1000 genomes]
rs12148735	0.90[ASN][1000 genomes]
rs12323999	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12324572	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12324584	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12440854	0.89[EUR][1000 genomes]
rs12905772	0.97[ASN][1000 genomes]
rs1549523	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1549525	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16957627	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16957630	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16957632	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1837959	0.85[ASN][1000 genomes]
rs1837960	0.85[ASN][1000 genomes]
rs2012467	0.88[ASN][1000 genomes]
rs2242068	0.82[ASN][1000 genomes]
rs2243434	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2244746	0.84[ASN][1000 genomes]
rs2245908	0.82[AMR][1000 genomes]
rs2254321	0.81[AMR][1000 genomes]
rs2254325	0.81[AMR][1000 genomes]
rs2278856	0.97[ASN][1000 genomes]
rs2278857	0.97[ASN][1000 genomes]
rs2278858	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2278859	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278860	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412778	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412779	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412780	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412781	0.95[ASN][1000 genomes]
rs2412782	0.88[ASN][1000 genomes]
rs2439841	0.80[AMR][1000 genomes]
rs2444028	0.82[AMR][1000 genomes]
rs2444029	0.82[AMR][1000 genomes]
rs2444036	0.87[ASN][1000 genomes]
rs2444247	0.82[AMR][1000 genomes]
rs2467733	0.87[ASN][1000 genomes]
rs2584700	0.81[ASN][1000 genomes]
rs2584701	0.90[ASN][1000 genomes]
rs2584702	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2584703	0.85[ASN][1000 genomes]
rs2584726	0.82[AMR][1000 genomes]
rs28415933	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28461955	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28578454	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28594657	0.83[EUR][1000 genomes]
rs28653441	0.93[ASN][1000 genomes]
rs28702649	0.97[ASN][1000 genomes]
rs28729853	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28758627	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2899082	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3213990	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3213991	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3742969	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742971	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3809481	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3809482	0.97[ASN][1000 genomes]
rs4075674	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4296223	0.95[ASN][1000 genomes]
rs4401024	0.95[ASN][1000 genomes]
rs4547312	0.97[ASN][1000 genomes]
rs4583210	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478028	1.00[ASN][1000 genomes]
rs478104	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs484029	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs484846	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs485148	0.85[ASN][1000 genomes]
rs488756	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs491648	0.82[AMR][1000 genomes]
rs491800	0.86[ASN][1000 genomes]
rs498837	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs499035	0.94[ASN][1000 genomes]
rs507178	1.00[ASN][1000 genomes]
rs510108	0.95[ASN][1000 genomes]
rs511673	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs512628	0.98[ASN][1000 genomes]
rs528517	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537115	0.81[AMR][1000 genomes]
rs550239	0.82[AMR][1000 genomes]
rs552701	1.00[ASN][1000 genomes]
rs558656	0.81[AMR][1000 genomes]
rs565007	0.82[AMR][1000 genomes]
rs573615	1.00[ASN][1000 genomes]
rs576557	0.92[ASN][1000 genomes]
rs6493081	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493082	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493083	0.97[ASN][1000 genomes]
rs6493084	0.97[ASN][1000 genomes]
rs6493085	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493086	0.97[ASN][1000 genomes]
rs6493087	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6493088	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs689835	0.81[AMR][1000 genomes]
rs690038	0.81[AMR][1000 genomes]
rs690263	0.82[AMR][1000 genomes]
rs690316	0.82[AMR][1000 genomes]
rs7163245	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7165471	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7166812	0.97[ASN][1000 genomes]
rs7167882	0.90[ASN][1000 genomes]
rs7168940	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7170152	0.91[ASN][1000 genomes]
rs7170489	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7172374	0.89[ASN][1000 genomes]
rs7175434	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7176849	0.90[ASN][1000 genomes]
rs8033714	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8039638	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8041132	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8042688	0.97[ASN][1000 genomes]
rs825739	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs825740	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs884704	0.88[ASN][1000 genomes]
rs933941	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs956391	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9920879	0.97[ASN][1000 genomes]
rs999026	0.88[ASN][1000 genomes]
rs999047	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs540031	ADAL	cis	multi-tissue	Pritchard
rs540031	ADAL	cis	Skin Sun Exposed Lower leg	GTEx
rs540031	ADAL	Cis_1M	lymphoblastoid	RTeQTL
rs540031	ADAL	cis	Esophagus Mucosa	GTEx
rs540031	ADAL	cis	Thyroid	GTEx
rs540031	CKMT1A	cis	Esophagus Mucosa	GTEx
rs540031	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs540031	ADAL	cis	Stomach	GTEx
rs540031	ADAL	cis	Artery Aorta	GTEx
rs540031	ADAL	cis	Heart Left Ventricle	GTEx
rs540031	ADAL	cis	Adipose Subcutaneous	GTEx
rs540031	ADAL	cis	Esophagus Muscularis	GTEx
rs540031	ADAL	cis	lung	GTEx
rs540031	ADAL	cis	Nerve Tibial	GTEx
rs540031	ADAL	cis	Artery Tibial	GTEx
rs540031	CATSPER2	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43607600-43609200	Enhancers	Fetal Stomach	stomach
2	chr15:43607800-43609000	Enhancers	Stomach Smooth Muscle	stomach
3	chr15:43608400-43609400	Bivalent Enhancer	HepG2	liver
4	chr15:43608600-43609000	Enhancers	Fetal Lung	lung
5	chr15:43608800-43610000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:43608800-43610200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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