Variant report

Variant	rs12340462
Chromosome Location	chr9:110246995-110246996
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:110243041..110245201-chr9:110246252..110249576,3	K562	blood:
2	chr9:110246852..110249468-chr9:110266978..110269904,2	MCF-7	breast:
3	chr9:110246539..110249058-chr9:111030937..111033862,2	MCF-7	breast:
4	chr9:110246480..110248143-chr9:110388562..110390733,2	MCF-7	breast:
5	chr9:110246511..110249498-chr9:111190126..111191677,2	MCF-7	breast:
6	chr9:110245261..110247030-chr9:111305318..111307225,2	MCF-7	breast:
7	chr9:110246319..110249443-chr9:111522237..111525040,3	MCF-7	breast:
8	chr9:110246498..110248989-chr9:110515168..110518438,3	MCF-7	breast:
9	chr9:110245244..110247953-chr9:110892992..110894889,2	MCF-7	breast:
10	chr9:110246472..110248757-chr9:111030906..111033731,4	MCF-7	breast:
11	chr9:110187314..110189202-chr9:110246490..110248123,2	MCF-7	breast:
12	chr9:110245030..110248029-chr9:110915233..110917839,2	MCF-7	breast:
13	chr9:110246045..110248500-chr9:111231689..111233848,2	MCF-7	breast:
14	chr9:110246769..110253919-chr9:110298442..110306182,20	MCF-7	breast:
15	chr9:110246987..110249540-chr9:110886248..110888523,2	MCF-7	breast:
16	chr9:110246354..110248073-chr9:110381109..110383476,2	MCF-7	breast:
17	chr9:110183651..110188912-chr9:110241760..110247233,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000227350	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10117763	0.88[EUR][1000 genomes]
rs10816519	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11788360	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11792359	1.00[EUR][1000 genomes]
rs11793219	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11794295	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11795298	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12335657	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12336189	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12336214	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12340310	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12345785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12351651	1.00[EUR][1000 genomes]
rs12352260	0.94[EUR][1000 genomes]
rs12353064	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34651589	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45463699	1.00[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110235600-110247600	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr9:110235800-110248400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr9:110236000-110248400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:110242200-110247400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:110242800-110247400	Weak transcription	Placenta	Placenta
6	chr9:110242800-110249000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:110243000-110249600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:110243200-110247200	Weak transcription	HMEC	breast
9	chr9:110243200-110247600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr9:110243200-110247800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:110243200-110247800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:110243200-110248000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr9:110243200-110248400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr9:110243200-110248800	Weak transcription	Fetal Lung	lung
15	chr9:110243400-110247400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:110243400-110247800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:110243600-110247200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr9:110243600-110247400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr9:110243600-110247800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr9:110243600-110247800	Weak transcription	Esophagus	oesophagus
21	chr9:110243600-110248000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:110243800-110247400	Weak transcription	Psoas Muscle	Psoas
23	chr9:110243800-110247400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr9:110243800-110247600	Weak transcription	Osteobl	bone
25	chr9:110244000-110247000	Weak transcription	NHEK	skin
26	chr9:110244000-110247200	Weak transcription	Hela-S3	cervix
27	chr9:110244000-110249200	Weak transcription	A549	lung
28	chr9:110244000-110250400	Weak transcription	HSMMtube	muscle
29	chr9:110244200-110248400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:110245600-110247400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr9:110245800-110247000	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr9:110246000-110249000	Weak transcription	Spleen	Spleen
33	chr9:110246000-110249800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:110246200-110247000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:110246200-110247200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:110246200-110247200	Weak transcription	Stomach Mucosa	stomach
37	chr9:110246200-110247400	Active TSS	NHDF-Ad	bronchial
38	chr9:110246200-110247600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr9:110246200-110253800	Active TSS	Right Atrium	heart
40	chr9:110246400-110247000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:110246600-110247000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:110246600-110247400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr9:110246600-110247400	Genic enhancers	Primary monocytes fromperipheralblood	blood
44	chr9:110246600-110247400	Active TSS	Rectal Mucosa Donor 31	rectum
45	chr9:110246600-110247600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr9:110246600-110249000	Weak transcription	Brain Anterior Caudate	brain
47	chr9:110246800-110247000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr9:110246800-110247000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:110246800-110247000	Active TSS	Ovary	ovary
50	chr9:110246800-110247000	Active TSS	Monocytes-CD14+_RO01746	blood

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