Variant report

Variant	rs1506678
Chromosome Location	chr12:45249492-45249493
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	chr12:45245058..45246783-chr12:45249459..45251550,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184613	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10506258	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs10785535	0.91[JPT][hapmap]
rs10785539	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880695	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880696	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880704	0.85[ASN][1000 genomes]
rs11182706	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11615964	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12822444	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs1376126	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1506676	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506679	0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs1506680	0.81[ASN][1000 genomes]
rs1876241	0.85[ASN][1000 genomes]
rs2408084	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs2408085	0.83[CHB][hapmap]
rs2465110	0.84[ASN][1000 genomes]
rs2658948	0.83[ASN][1000 genomes]
rs2658954	0.85[ASN][1000 genomes]
rs2939697	0.83[ASN][1000 genomes]
rs2939698	0.82[ASN][1000 genomes]
rs374144	0.91[JPT][hapmap]
rs7295923	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7304472	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7305124	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7952764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953663	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7963606	0.82[ASN][1000 genomes]
rs7979717	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378050	chr12:44963059-45264289	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv832394	chr12:45077573-45269305	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
3	nsv1036926	chr12:45131884-45273648	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv541484	chr12:45131884-45273648	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1506678	RP11-478B9.2	cis	Skin Sun Exposed Lower leg	GTEx
rs1506678	DBX2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45242800-45252200	Enhancers	Primary T helper naive cells from peripheral blood	blood
2	chr12:45243800-45250600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:45243800-45251600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:45246600-45250200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr12:45247400-45253600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr12:45247800-45250200	Weak transcription	Fetal Brain Female	brain
7	chr12:45247800-45251400	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr12:45248400-45250400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr12:45248400-45252400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:45248600-45259600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:45248800-45255800	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr12:45249000-45250400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:45249000-45252400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr12:45249000-45255400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr12:45249200-45251000	Weak transcription	Fetal Brain Male	brain
16	chr12:45249200-45252400	Enhancers	Primary T cells from cord blood	blood

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