Variant report

Variant	rs3946273
Chromosome Location	chr3:160365382-160365383
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160166590..160168734-chr3:160364883..160367171,2	K562	blood:
2	chr3:160334651..160337629-chr3:160364585..160366181,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213186	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10936207	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10936208	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10936209	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11709300	0.83[EUR][1000 genomes]
rs13065289	0.81[EUR][1000 genomes]
rs13095931	0.95[EUR][1000 genomes]
rs1317085	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17236586	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2178452	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28544045	0.95[EUR][1000 genomes]
rs28730907	0.94[EUR][1000 genomes]
rs34362576	0.94[EUR][1000 genomes]
rs34949451	0.94[EUR][1000 genomes]
rs35308461	0.93[EUR][1000 genomes]
rs35480231	0.93[EUR][1000 genomes]
rs35664264	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35867836	0.93[EUR][1000 genomes]
rs36118017	0.94[EUR][1000 genomes]
rs4679659	0.95[EUR][1000 genomes]
rs4679660	0.94[EUR][1000 genomes]
rs4679909	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4679910	0.84[EUR][1000 genomes]
rs62272215	0.83[EUR][1000 genomes]
rs62272216	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62272217	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62272218	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62272219	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62272220	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6773389	0.94[EUR][1000 genomes]
rs6773962	0.83[EUR][1000 genomes]
rs6774379	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6774566	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6776873	0.94[EUR][1000 genomes]
rs6777739	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6779581	0.94[EUR][1000 genomes]
rs6779671	0.94[EUR][1000 genomes]
rs6787452	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6797760	0.94[EUR][1000 genomes]
rs6798462	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6801373	0.94[EUR][1000 genomes]
rs7632884	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	nsv877703	chr3:160325458-160398885	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	esv2757019	chr3:160351021-160380161	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv2759194	chr3:160351021-160380161	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv10343	chr3:160355620-160366624	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	esv3463584	chr3:160355760-160366323	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv3463585	chr3:160355760-160366323	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv822307	chr3:160355841-160366230	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3946273	SMC4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160364800-160366200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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