Variant report

Variant	rs2814060
Chromosome Location	chr1:227722228-227722229
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227721387..227723792-chr1:227750003..227751668,2	MCF-7	breast:
2	chr1:227721537..227724263-chr1:227727527..227730135,2	MCF-7	breast:
3	chr1:227699513..227702199-chr1:227720616..227723558,2	K562	blood:

Variant related genes	Relation type
ENSG00000181450	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10047205	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10916178	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10916192	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12059899	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12069550	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12070539	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12080590	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12082414	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12092295	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12095502	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12096675	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1495846	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1495849	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16847966	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16847991	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16847992	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16848029	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1923821	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2012432	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2132366	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2256599	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2453682	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2644143	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2644144	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2644145	0.81[ASN][1000 genomes]
rs2644146	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2644153	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2644161	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2814059	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814061	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2814084	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814085	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2819496	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2819498	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819507	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2819511	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3748806	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4376731	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4589104	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58020705	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59034043	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59149651	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59753688	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61343450	0.83[EUR][1000 genomes]
rs66471275	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66491073	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6659745	0.89[EUR][1000 genomes]
rs66736638	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6688145	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6693348	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66938123	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67216605	0.83[EUR][1000 genomes]
rs67511833	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67676707	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs68046179	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs68186506	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72632830	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72632831	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72632832	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72748074	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7413796	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs753541	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7539151	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs903692	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs903693	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs903694	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs903695	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs965942	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv873244	chr1:227682414-227736363	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv873247	chr1:227697381-227736363	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv873248	chr1:227710381-227786033	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv945338	chr1:227712483-227722545	ZNF genes & repeats Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2814060	ZNF678	Cis_1M	lymphoblastoid	RTeQTL
rs2814060	C1orf142	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227718600-227723200	Weak transcription	Psoas Muscle	Psoas
2	chr1:227720800-227725800	Weak transcription	Pancreas	Pancrea
3	chr1:227720800-227729200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:227720800-227729200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:227721200-227725800	Weak transcription	Aorta	Aorta

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