Variant report

Variant	rs2997678
Chromosome Location	chr9:72686096-72686097
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	chr6:30582912..30585021-chr9:72685079..72686915,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222894	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1007127	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10481740	0.93[ASN][1000 genomes]
rs10481741	0.93[ASN][1000 genomes]
rs10735583	0.93[ASN][1000 genomes]
rs10780811	0.93[ASN][1000 genomes]
rs1536956	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs1927106	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1927115	0.87[ASN][1000 genomes]
rs2148861	0.87[ASN][1000 genomes]
rs2209779	0.91[ASN][1000 genomes]
rs2281935	0.82[ASN][1000 genomes]
rs2975862	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2975890	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2975907	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2975908	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2975910	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2975915	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2975917	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2997652	0.86[ASN][1000 genomes]
rs2997664	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2997676	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2997677	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015168	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3015224	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3015232	0.91[ASN][1000 genomes]
rs3015238	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3015242	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744968	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744977	0.93[ASN][1000 genomes]
rs4744978	0.93[ASN][1000 genomes]
rs7027209	0.94[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1049457	chr9:72539144-72765913	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv831613	chr9:72586058-72740061	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72667600-72688400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr9:72670000-72688400	Weak transcription	NH-A	brain
3	chr9:72676600-72694000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr9:72676800-72688200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr9:72676800-72688400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:72677000-72689000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:72677600-72694000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:72680000-72689200	Enhancers	Colon Smooth Muscle	Colon
9	chr9:72681000-72687600	Enhancers	Rectal Smooth Muscle	rectum
10	chr9:72683400-72686600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:72683400-72688000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:72683400-72688200	Weak transcription	Osteobl	bone
13	chr9:72684800-72694000	Weak transcription	Adipose Nuclei	Adipose
14	chr9:72685000-72687400	Weak transcription	HSMM	muscle
15	chr9:72685000-72694600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr9:72685200-72687200	Weak transcription	HSMMtube	muscle
17	chr9:72685200-72688600	Weak transcription	Ovary	ovary
18	chr9:72685200-72689000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:72685200-72689200	Weak transcription	Fetal Stomach	stomach
20	chr9:72685200-72692200	Weak transcription	Small Intestine	intestine
21	chr9:72685200-72695800	Weak transcription	Aorta	Aorta
22	chr9:72685200-72696000	Weak transcription	Right Atrium	heart
23	chr9:72685400-72688400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:72685400-72690400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr9:72685800-72686600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:72685800-72686600	Enhancers	Stomach Smooth Muscle	stomach

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