Variant report

Variant	rs12341669
Chromosome Location	chr9:116055566-116055567
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116053533..116057735-chr9:116058068..116062323,4	K562	blood:
2	chr9:116037887..116040476-chr9:116055081..116056645,2	K562	blood:
3	chr9:116037155..116039371-chr9:116054737..116056807,2	MCF-7	breast:
4	chr9:116036914..116039387-chr9:116053973..116056581,2	K562	blood:
5	chr9:116040816..116043604-chr9:116053312..116056081,3	MCF-7	breast:
6	chr9:116054929..116058723-chr9:116059143..116063371,5	MCF-7	breast:
7	chr9:116054553..116056753-chr9:116171016..116173087,2	MCF-7	breast:
8	chr9:116053475..116056879-chr9:116057829..116061617,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000136875	Chromatin interaction
ENSG00000176386	Chromatin interaction
ENSG00000165188	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000157653	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10817469	0.80[EUR][1000 genomes]
rs10817471	0.80[EUR][1000 genomes]
rs10817472	0.80[EUR][1000 genomes]
rs10981705	0.80[EUR][1000 genomes]
rs12336832	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12342197	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342549	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343330	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12348629	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12349495	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12349500	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12349614	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12351168	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351630	0.95[ASN][1000 genomes]
rs12352784	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12352925	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17831256	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28733164	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58402825	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66509679	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7863910	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116038800-116060000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:116039000-116056800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:116039000-116058200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:116039400-116055800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:116039400-116056200	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr9:116039400-116056400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:116039400-116056400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:116039400-116056400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr9:116039400-116056400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:116039400-116056600	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr9:116039400-116056600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:116039400-116056600	Strong transcription	Primary B cells from peripheral blood	blood
13	chr9:116039400-116056600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:116039400-116056600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:116039400-116056600	Strong transcription	Placenta	Placenta
16	chr9:116039400-116056600	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr9:116039400-116056600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr9:116039400-116056800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:116039400-116056800	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr9:116039600-116055600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:116039600-116055800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
22	chr9:116039600-116056000	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr9:116039600-116056000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:116039600-116056200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr9:116039600-116056400	Strong transcription	Fetal Lung	lung
26	chr9:116039600-116056600	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr9:116039600-116056800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr9:116039600-116056800	Strong transcription	Fetal Stomach	stomach
29	chr9:116040000-116055800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr9:116040000-116056000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr9:116040000-116056400	Strong transcription	NH-A	brain
32	chr9:116040000-116056800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr9:116040200-116056000	Strong transcription	HSMM	muscle
34	chr9:116040200-116056000	Strong transcription	NHEK	skin
35	chr9:116040200-116056200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr9:116040400-116055600	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr9:116040400-116055800	Strong transcription	Adipose Nuclei	Adipose
38	chr9:116040400-116056200	Strong transcription	Primary B cells from cord blood	blood
39	chr9:116040400-116056200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr9:116040400-116056200	Strong transcription	HMEC	breast
41	chr9:116040400-116056600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:116040400-116056800	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr9:116040400-116056800	Strong transcription	Fetal Thymus	thymus
44	chr9:116040600-116056200	Strong transcription	Brain Hippocampus Middle	brain
45	chr9:116040600-116056800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:116040800-116055600	Strong transcription	Brain Substantia Nigra	brain
47	chr9:116040800-116055800	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr9:116040800-116056000	Strong transcription	Osteobl	bone
49	chr9:116040800-116056200	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr9:116040800-116056200	Strong transcription	Stomach Smooth Muscle	stomach

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