Variant report

Variant	rs13075424
Chromosome Location	chr3:160359065-160359066
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160263639..160265252-chr3:160357091..160359879,2	K562	blood:
2	chr3:160158711..160161195-chr3:160357597..160359673,2	K562	blood:
3	chr3:160284019..160287638-chr3:160358155..160361126,3	K562	blood:

Variant related genes	Relation type
ENSG00000229320	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10460866	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11711627	0.91[ASN][1000 genomes]
rs11712392	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11713230	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11720693	0.91[EUR][1000 genomes]
rs11721112	0.81[ASN][1000 genomes]
rs13062928	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13065269	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13072556	0.88[EUR][1000 genomes]
rs13074231	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13085507	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1882125	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1920650	0.91[ASN][1000 genomes]
rs1920663	0.81[ASN][1000 genomes]
rs2141668	0.91[ASN][1000 genomes]
rs2178451	0.88[ASN][1000 genomes]
rs2367209	0.81[EUR][1000 genomes]
rs34058107	0.90[EUR][1000 genomes]
rs34444753	0.86[EUR][1000 genomes]
rs35008770	0.91[ASN][1000 genomes]
rs35498840	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4679903	0.91[ASN][1000 genomes]
rs4679904	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57718211	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60339919	0.86[EUR][1000 genomes]
rs6792943	0.86[EUR][1000 genomes]
rs71314011	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7633839	0.91[EUR][1000 genomes]
rs7634255	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7644186	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	esv2755769	chr3:160352298-160359298	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv10343	chr3:160355620-160366624	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv3463584	chr3:160355760-160366323	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv3463585	chr3:160355760-160366323	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv822307	chr3:160355841-160366230	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv441846	chr3:160356940-160359109	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv34627	chr3:160356940-160359298	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv2421521	chr3:160356940-160362285	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	esv2763313	chr3:160356940-160362285	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13075424	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160355400-160359600	Weak transcription	NH-A	brain
2	chr3:160358200-160361000	Enhancers	Hela-S3	cervix
3	chr3:160358800-160360400	Enhancers	HUVEC	blood vessel
4	chr3:160359000-160360400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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