Variant report

Variant	rs12685082
Chromosome Location	chr9:15554620-15554621
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	chr9:15509318..15512022-chr9:15550389..15555494,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164985	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10283923	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10756687	1.00[YRI][hapmap]
rs10756690	1.00[YRI][hapmap]
rs10810401	1.00[YRI][hapmap]
rs10962048	1.00[JPT][hapmap]
rs12336509	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12339417	1.00[JPT][hapmap]
rs12380487	1.00[CHB][hapmap]
rs12682808	0.85[ASN][1000 genomes]
rs13288118	0.82[CHB][hapmap]
rs1396705	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1533040	1.00[YRI][hapmap]
rs16933311	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs16933316	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs16933318	1.00[JPT][hapmap]
rs16933504	1.00[JPT][hapmap]
rs16933544	1.00[JPT][hapmap]
rs2175082	1.00[YRI][hapmap]
rs276452	0.92[ASN][1000 genomes]
rs4372097	0.82[CHB][hapmap]
rs4740615	1.00[YRI][hapmap]
rs6474950	0.84[AFR][1000 genomes]
rs7021778	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7032595	1.00[JPT][hapmap]
rs7035048	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7036674	1.00[YRI][hapmap]
rs73410238	0.83[AFR][1000 genomes]
rs73410242	0.83[AFR][1000 genomes]
rs73410253	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs73410254	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs73410286	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73416209	0.84[AFR][1000 genomes]
rs7846818	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7857933	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7860283	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7862428	1.00[JPT][hapmap]
rs7863046	0.82[CHB][hapmap]
rs7873842	0.87[AFR][1000 genomes]
rs906798	0.85[AFR][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	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv892629	chr9:15516375-15634326	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3407839	chr9:15530438-15665653	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15553200-15555000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:15553600-15554800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr9:15553800-15576200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr9:15553800-15580600	Weak transcription	Ovary	ovary
5	chr9:15553800-15592600	Weak transcription	Left Ventricle	heart
6	chr9:15554000-15554800	Active TSS	Duodenum Mucosa	Duodenum
7	chr9:15554000-15554800	Enhancers	Dnd41	blood
8	chr9:15554000-15564400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr9:15554000-15590200	Weak transcription	Fetal Stomach	stomach
10	chr9:15554200-15554800	Flanking Active TSS	GM12878-XiMat	blood
11	chr9:15554400-15554800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:15554400-15579400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr9:15554600-15554800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr9:15554600-15554800	Enhancers	Primary hematopoietic stem cells	blood
15	chr9:15554600-15554800	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr9:15554600-15555000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:15554600-15555600	Enhancers	Thymus	Thymus
18	chr9:15554600-15556400	Weak transcription	Fetal Brain Male	brain
19	chr9:15554600-15563600	Weak transcription	Fetal Thymus	thymus
20	chr9:15554600-15580800	Weak transcription	Brain Anterior Caudate	brain

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