Variant report

Variant	rs1906717
Chromosome Location	chr12:48768774-48768775
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48743253..48745625-chr12:48768325..48770230,2	MCF-7	breast:
2	chr12:48764324..48767170-chr12:48768369..48771517,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257735	Chromatin interaction
ENSG00000167528	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1074174	0.86[CEU][hapmap]
rs10783235	0.85[JPT][hapmap]
rs10783249	0.89[ASN][1000 genomes]
rs10875798	0.86[JPT][hapmap]
rs11168438	0.81[JPT][hapmap]
rs11168458	0.86[JPT][hapmap]
rs11168541	0.84[JPT][hapmap]
rs12426877	0.82[JPT][hapmap]
rs12822431	0.86[JPT][hapmap]
rs12831063	0.86[JPT][hapmap]
rs2054902	0.88[CEU][hapmap]
rs2261608	0.86[JPT][hapmap]
rs2291483	0.86[JPT][hapmap]
rs2468950	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2634669	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2634679	0.88[CEU][hapmap]
rs2634685	1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2732458	0.88[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2732459	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2732482	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2932090	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2932091	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3752820	0.86[JPT][hapmap]
rs7301176	0.86[JPT][hapmap]
rs901962	0.88[CEU][hapmap];0.80[TSI][hapmap]
rs901963	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv826362	chr12:48693048-48768853	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv975606	chr12:48748764-48784504	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1906717	ZNF641	cis	Whole Blood	GTEx
rs1906717	TMEM117	cis	cerebellum	SCAN
rs1906717	ZNF641	cis	Muscle Skeletal	GTEx
rs1906717	TMEM106C	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
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