Variant report

Variant	rs10782820
Chromosome Location	chr1:84257951-84257952
allele	C/G
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	STAT3	chr1:84257711-84258082	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr1:84257658-84258074	MCF10A-Er-Src	breast:	n/a	chr1:84257682-84257693
3	FOS	chr1:84257813-84257970	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr1:84257654-84258096	MCF10A-Er-Src	breast:	n/a	chr1:84257682-84257693
5	MYC	chr1:84257900-84257970	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr1:84257657-84258097	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr1:84257675-84258059	MCF10A-Er-Src	breast:	n/a	chr1:84257682-84257693
8	STAT3	chr1:84257672-84258086	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000223231	TF binding region

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10157076	0.84[ASN][1000 genomes]
rs10158343	0.86[ASN][1000 genomes]
rs1040576	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10430047	0.87[ASN][1000 genomes]
rs10430048	1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs10430063	0.87[ASN][1000 genomes]
rs10430064	0.87[ASN][1000 genomes]
rs10465742	0.86[ASN][1000 genomes]
rs10489502	0.83[ASN][1000 genomes]
rs10489503	0.83[ASN][1000 genomes]
rs10489504	0.84[ASN][1000 genomes]
rs10489506	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10489507	0.86[ASN][1000 genomes]
rs10874420	0.84[ASN][1000 genomes]
rs10874421	0.87[ASN][1000 genomes]
rs10874422	0.87[ASN][1000 genomes]
rs11163828	0.83[ASN][1000 genomes]
rs11163829	0.83[ASN][1000 genomes]
rs11163830	0.83[ASN][1000 genomes]
rs11163832	0.87[ASN][1000 genomes]
rs11163833	0.87[ASN][1000 genomes]
rs11163835	0.87[ASN][1000 genomes]
rs11163837	0.87[ASN][1000 genomes]
rs11163838	0.87[ASN][1000 genomes]
rs11163839	0.87[ASN][1000 genomes]
rs11163840	1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs11163841	0.85[ASN][1000 genomes]
rs11163842	0.87[ASN][1000 genomes]
rs11163847	0.86[ASN][1000 genomes]
rs11163848	0.86[ASN][1000 genomes]
rs11163850	0.86[ASN][1000 genomes]
rs11163853	0.82[ASN][1000 genomes]
rs11163854	0.82[ASN][1000 genomes]
rs12028642	0.86[ASN][1000 genomes]
rs12029461	0.86[ASN][1000 genomes]
rs12033157	0.86[ASN][1000 genomes]
rs12033859	0.81[ASN][1000 genomes]
rs12035289	0.83[ASN][1000 genomes]
rs12041369	0.84[ASN][1000 genomes]
rs12044606	0.87[ASN][1000 genomes]
rs12045391	0.87[ASN][1000 genomes]
rs12048434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12057556	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12059428	0.87[ASN][1000 genomes]
rs12067203	0.81[ASN][1000 genomes]
rs12069168	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12070108	0.82[ASN][1000 genomes]
rs12071975	0.82[ASN][1000 genomes]
rs12080974	0.87[ASN][1000 genomes]
rs12082383	0.81[ASN][1000 genomes]
rs12082518	0.82[ASN][1000 genomes]
rs12085122	0.87[ASN][1000 genomes]
rs12085367	0.82[ASN][1000 genomes]
rs12087099	0.87[ASN][1000 genomes]
rs12088221	0.87[ASN][1000 genomes]
rs12088867	0.87[ASN][1000 genomes]
rs12091588	0.87[ASN][1000 genomes]
rs12092736	0.87[ASN][1000 genomes]
rs12093748	0.83[ASN][1000 genomes]
rs17129275	0.83[ASN][1000 genomes]
rs17129297	0.83[ASN][1000 genomes]
rs17129321	0.83[ASN][1000 genomes]
rs17129344	0.83[ASN][1000 genomes]
rs17129346	0.83[ASN][1000 genomes]
rs17129416	0.87[ASN][1000 genomes]
rs17129475	0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17129836	0.82[ASN][1000 genomes]
rs17129848	0.82[ASN][1000 genomes]
rs17129850	0.82[ASN][1000 genomes]
rs17129859	0.81[ASN][1000 genomes]
rs17129909	0.81[ASN][1000 genomes]
rs1951928	0.86[ASN][1000 genomes]
rs2057084	0.81[ASN][1000 genomes]
rs2179763	0.84[EUR][1000 genomes]
rs28476757	0.87[ASN][1000 genomes]
rs35299117	0.86[ASN][1000 genomes]
rs4001468	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4140461	0.87[ASN][1000 genomes]
rs55958267	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60743554	0.82[ASN][1000 genomes]
rs60860789	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61766224	0.83[ASN][1000 genomes]
rs61767991	0.86[ASN][1000 genomes]
rs61767992	0.86[ASN][1000 genomes]
rs61767993	0.82[ASN][1000 genomes]
rs714280	0.87[ASN][1000 genomes]
rs717234	0.87[ASN][1000 genomes]
rs72952444	0.87[ASN][1000 genomes]
rs742779	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7529582	0.84[ASN][1000 genomes]
rs969125	0.87[ASN][1000 genomes]
rs969126	0.87[ASN][1000 genomes]
rs997869	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	nsv947189	chr1:84257762-84263159	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10782820	LPHN2	cis	cerebellum	SCAN
rs10782820	CLCA3P	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84255400-84264600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:84257000-84261600	Weak transcription	Primary T cells from cord blood	blood
3	chr1:84257200-84258200	Enhancers	NHDF-Ad	bronchial
4	chr1:84257200-84258400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:84257200-84258400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:84257400-84258000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:84257400-84258400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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