Variant report

Variant	rs12217109
Chromosome Location	chr1:153433068-153433069
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	chr1:153327739..153331289-chr1:153432933..153435895,3	MCF-7	breast:
2	chr1:153329373..153332340-chr1:153432969..153437036,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163220	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10888560	0.81[AMR][1000 genomes]
rs11205297	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs12022550	0.88[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap]
rs12025638	0.88[JPT][hapmap];0.92[YRI][hapmap]
rs12034788	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12043280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs12043556	1.00[CHB][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12044034	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12044491	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12045252	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12047203	0.87[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12047494	0.89[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs16835332	0.89[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap]
rs2986209	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs3014848	0.88[JPT][hapmap]
rs41265152	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55668683	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs55703007	0.96[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs56009204	0.88[ASN][1000 genomes]
rs72708746	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
6	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases
7	nsv946399	chr1:153431838-153438343	Enhancers Bivalent Enhancer Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153431000-153439000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:153432800-153433200	Enhancers	Esophagus	oesophagus

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