Variant report

Variant	rs10879928
Chromosome Location	chr12:75925776-75925777
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75925641..75928428-chr12:76424278..76425852,2	K562	blood:
2	chr12:75924261..75926963-chr12:76425587..76427776,2	MCF-7	breast:
3	chr12:75923805..75926647-chr12:76427379..76430609,3	MCF-7	breast:
4	chr12:75924745..75926908-chr12:75978244..75979819,2	MCF-7	breast:
5	chr12:75923131..75928282-chr12:76423369..76427377,5	MCF-7	breast:

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

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1148003	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1148004	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1148005	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1148006	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1275474	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1275478	0.84[CHD][hapmap];0.83[GIH][hapmap];0.83[LWK][hapmap]
rs1275481	0.86[CHD][hapmap];0.81[GIH][hapmap];0.91[LWK][hapmap]
rs1552040	0.83[AFR][1000 genomes]
rs1679381	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1697752	0.84[CHD][hapmap];0.81[GIH][hapmap];0.91[LWK][hapmap]
rs1697754	0.84[CHD][hapmap];0.91[LWK][hapmap]
rs1795379	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1824980	0.90[ASN][1000 genomes]
rs1824982	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2366987	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704766	0.84[CHD][hapmap];0.81[GIH][hapmap];0.91[LWK][hapmap]
rs2704767	0.84[CHD][hapmap];0.81[GIH][hapmap];0.91[LWK][hapmap]
rs3847669	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3858534	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3912214	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv428592	chr12:75766619-75936721	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	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
7	nsv470305	chr12:75896688-75987360	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10879928	GLIPR1L2	cis	parietal	SCAN
rs10879928	GLIPR1	cis	cerebellum	SCAN
rs10879928	GLIPR1L2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75922800-75927200	Weak transcription	HSMMtube	muscle

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