Variant report

Variant	rs7866017
Chromosome Location	chr9:2569631-2569632
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	chr9:2567610..2570420-chr9:2620713..2623138,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236404	Chromatin interaction
ENSG00000147852	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12000322	1.00[AMR][1000 genomes]
rs1512716	0.89[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7040200	1.00[MEX][hapmap]
rs7866442	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers 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 miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv466078	chr9:2218129-2621030	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv613126	chr9:2218129-2621030	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv529508	chr9:2267812-2684272	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv466081	chr9:2353522-2596783	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv613132	chr9:2353522-2596783	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv892066	chr9:2397564-2589739	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv531564	chr9:2452325-2700375	Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv1033424	chr9:2508296-2575408	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1029876	chr9:2526760-2633562	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv892068	chr9:2543888-2589739	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7866017	MYO6	trans	lymphoblastoid	seeQTL
rs7866017	DAPK2	trans	lymphoblastoid	seeQTL
rs7866017	SLC12A8	trans	lymphoblastoid	seeQTL
rs7866017	BAG3	trans	lymphoblastoid	seeQTL
rs7866017	CD38	trans	lymphoblastoid	seeQTL
rs7866017	SERPINB9	trans	lymphoblastoid	seeQTL
rs7866017	SMARCA2	cis	lymphoblastoid	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2559600-2570600	Weak transcription	Aorta	Aorta
2	chr9:2559800-2577000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:2560800-2570800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr9:2561000-2570600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:2564400-2570600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:2566200-2570800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:2566400-2571800	Enhancers	Adipose Nuclei	Adipose
8	chr9:2567000-2571200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr9:2567000-2571800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:2567600-2577600	Enhancers	Fetal Heart	heart
11	chr9:2567800-2569800	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr9:2568400-2570600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:2568400-2570800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:2568400-2570800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:2568400-2570800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr9:2568600-2570600	Weak transcription	Stomach Mucosa	stomach
17	chr9:2568600-2570800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:2568600-2576000	Enhancers	Ovary	ovary
19	chr9:2568800-2570600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:2568800-2570600	Weak transcription	Right Atrium	heart
21	chr9:2569000-2570000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:2569000-2570000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr9:2569000-2570600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr9:2569000-2570600	Weak transcription	Fetal Muscle Leg	muscle
25	chr9:2569000-2570600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr9:2569000-2570600	Weak transcription	A549	lung
27	chr9:2569000-2570600	Weak transcription	HMEC	breast
28	chr9:2569000-2571200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr9:2569000-2572400	Weak transcription	Left Ventricle	heart
30	chr9:2569000-2575400	Weak transcription	Right Ventricle	heart
31	chr9:2569200-2570000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr9:2569200-2570600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr9:2569200-2570600	Weak transcription	Hela-S3	cervix
34	chr9:2569200-2571000	Weak transcription	HSMMtube	muscle
35	chr9:2569200-2571200	Weak transcription	Psoas Muscle	Psoas
36	chr9:2569400-2571000	Weak transcription	HSMM	muscle
37	chr9:2569600-2569800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr9:2569600-2571600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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