Variant report

Variant	rs12420961
Chromosome Location	chr11:92864441-92864442
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:92862981..92865243-chr11:92958375..92960659,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10466352	0.89[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10501802	0.83[ASN][1000 genomes]
rs10765587	0.89[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10830982	0.84[ASN][1000 genomes]
rs10830983	0.83[ASN][1000 genomes]
rs10830988	0.89[CHB][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs10830989	0.89[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10830996	0.89[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10831004	0.85[ASN][1000 genomes]
rs10831006	0.85[ASN][1000 genomes]
rs12786007	0.93[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap]
rs1348871	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1508608	0.89[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1508610	0.83[ASN][1000 genomes]
rs1508611	0.84[ASN][1000 genomes]
rs1562366	0.83[ASN][1000 genomes]
rs1992803	0.81[JPT][hapmap]
rs2121468	0.82[GIH][hapmap];0.81[JPT][hapmap]
rs4753436	0.89[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs522508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546386	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7110304	0.85[ASN][1000 genomes]
rs7130429	0.81[ASN][1000 genomes]
rs7925288	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs990660	0.84[ASN][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	nsv555903	chr11:92640787-92877533	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv555904	chr11:92640787-92881933	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1039134	chr11:92790000-93219942	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv525304	chr11:92829904-92877533	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv435	chr11:92853766-92887893	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12420961	SLC36A4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:92860000-92869600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:92861800-92866800	Weak transcription	NHLF	lung
3	chr11:92862800-92880400	Weak transcription	Aorta	Aorta
4	chr11:92864200-92876400	Weak transcription	Monocytes-CD14+_RO01746	blood

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