Variant report

Variant	rs11180600
Chromosome Location	chr12:76015466-76015467
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:76015220..76016961-chr12:76477481..76480006,2	MCF-7	breast:
2	chr12:76013741..76020372-chr12:76422912..76427305,12	MCF-7	breast:
3	chr12:76014354..76029119-chr12:76417641..76428409,36	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257839	Chromatin interaction
ENSG00000187109	Chromatin interaction
ENSG00000139289	Chromatin interaction
ENSG00000257453	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10748283	0.82[ASN][1000 genomes]
rs10748284	0.81[ASN][1000 genomes]
rs10785199	0.84[ASN][1000 genomes]
rs10785200	0.84[ASN][1000 genomes]
rs10879937	0.82[ASN][1000 genomes]
rs10879938	0.92[ASN][1000 genomes]
rs10879943	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10879944	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10879945	0.83[ASN][1000 genomes]
rs10879946	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10879947	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10879948	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11180601	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11180605	0.82[ASN][1000 genomes]
rs11495681	0.83[ASN][1000 genomes]
rs12310185	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12318049	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1480005	0.93[ASN][1000 genomes]
rs1871548	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34767748	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34952545	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4882601	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4882602	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4882637	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4882639	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4882640	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7958075	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7958490	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7958760	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7973399	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7980645	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11180600	RP11-585P4.5	cis	Thyroid	GTEx
rs11180600	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs11180600	GLIPR1L2	cis	Thyroid	GTEx
rs11180600	GLIPR1L2	cis	Artery Tibial	GTEx
rs11180600	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75980000-76017000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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