Variant report

Variant	rs12658097
Chromosome Location	chr5:1640282-1640283
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1634031..1636577-chr5:1639531..1641911,4	MCF-7	breast:
2	chr5:1632420..1636449-chr5:1636560..1641821,6	MCF-7	breast:
3	chr5:1475367..1477969-chr5:1638035..1640520,2	MCF-7	breast:
4	chr5:1637235..1639210-chr5:1639365..1642347,2	K562	blood:

Variant related genes	Relation type
ENSG00000188002	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10074606	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11133842	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11747600	0.88[ASN][1000 genomes]
rs12658927	0.94[ASN][1000 genomes]
rs13158448	0.94[ASN][1000 genomes]
rs13181671	0.95[ASN][1000 genomes]
rs1875193	0.82[AMR][1000 genomes]
rs1968011	0.91[ASN][1000 genomes]
rs2354149	0.84[ASN][1000 genomes]
rs34192949	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4975672	0.89[ASN][1000 genomes]
rs4975674	0.91[ASN][1000 genomes]
rs4975675	0.90[ASN][1000 genomes]
rs4975678	0.93[ASN][1000 genomes]
rs4975679	0.95[ASN][1000 genomes]
rs4975681	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55916019	0.80[AMR][1000 genomes]
rs6867862	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6870197	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6881649	0.84[ASN][1000 genomes]
rs6884329	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7717798	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7724533	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv880740	chr5:1468287-1671200	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
3	nsv881554	chr5:1468287-1696932	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
4	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
5	nsv881096	chr5:1503610-1671200	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
6	nsv880390	chr5:1612612-1653418	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv880788	chr5:1629407-1671200	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv881328	chr5:1637461-1671200	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv968136	chr5:1640086-1641086	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12658097	LOC728613	Cis_1M	lymphoblastoid	RTeQTL
rs12658097	LOC728613///PDCD6	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1634600-1645000	Weak transcription	Right Atrium	heart
2	chr5:1634600-1645200	Weak transcription	Gastric	stomach
3	chr5:1639200-1640400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:1640000-1640800	Bivalent Enhancer	Fetal Muscle Leg	muscle
5	chr5:1640000-1641400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:1640000-1642400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:1640000-1642800	Enhancers	H1 Cell Line	embryonic stem cell

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