Variant report

Variant	rs12378850
Chromosome Location	chr9:108063472-108063473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108057913..108059499-chr9:108062529..108064891,2	MCF-7	breast:
2	chr9:108061298..108064082-chr9:108078853..108080505,2	K562	blood:
3	chr9:108044800..108047623-chr9:108061922..108064222,3	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10991609	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2297022	1.00[MEX][hapmap]
rs327989	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs328009	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs328016	1.00[ASW][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs384825	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs388909	1.00[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs391232	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs391386	1.00[EUR][1000 genomes]
rs4387039	1.00[CHD][hapmap]
rs451915	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479307	1.00[GIH][hapmap]
rs7035065	1.00[GIH][hapmap]
rs7858401	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893685	chr9:107940737-108083485	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv893686	chr9:107968330-108083485	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893687	chr9:107973277-108083485	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv893688	chr9:107974761-108083485	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv893689	chr9:107978563-108130606	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv893690	chr9:107992706-108083485	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108049400-108074200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:108054000-108065400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:108054000-108070000	Weak transcription	Gastric	stomach
4	chr9:108054600-108090800	Weak transcription	Psoas Muscle	Psoas
5	chr9:108055200-108065000	Weak transcription	Primary B cells from cord blood	blood
6	chr9:108055600-108151200	Weak transcription	Esophagus	oesophagus
7	chr9:108056800-108077800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr9:108057000-108064200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr9:108057000-108066800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr9:108057400-108082600	Weak transcription	Dnd41	blood
11	chr9:108059200-108065800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr9:108059400-108081200	Weak transcription	Fetal Kidney	kidney
13	chr9:108060000-108075000	Weak transcription	Ovary	ovary
14	chr9:108060200-108077000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr9:108060400-108068200	Weak transcription	Fetal Heart	heart
16	chr9:108060600-108071000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:108061000-108069600	Weak transcription	Fetal Brain Male	brain
18	chr9:108061200-108066400	Strong transcription	Primary T cells from cord blood	blood
19	chr9:108061400-108063600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:108061400-108063800	Strong transcription	Fetal Lung	lung
21	chr9:108061400-108064000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:108061600-108063600	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr9:108061600-108063800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr9:108061600-108066200	Genic enhancers	Brain Cingulate Gyrus	brain
25	chr9:108061800-108063800	Enhancers	Hela-S3	cervix
26	chr9:108061800-108066200	Genic enhancers	Brain Inferior Temporal Lobe	brain
27	chr9:108062000-108063600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr9:108062000-108067000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr9:108062200-108063800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr9:108062200-108064600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr9:108062200-108066600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr9:108062200-108069600	Weak transcription	Pancreas	Pancrea
33	chr9:108062200-108069800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr9:108062200-108071000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:108062200-108071800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr9:108062200-108071800	Weak transcription	NHEK	skin
37	chr9:108062200-108072000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:108062200-108076400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr9:108062200-108077400	Weak transcription	Thymus	Thymus
40	chr9:108062200-108084000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr9:108062200-108091400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr9:108062200-108091800	Weak transcription	Aorta	Aorta
43	chr9:108062200-108098800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr9:108062400-108064000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr9:108062400-108066000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr9:108062400-108070000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr9:108062400-108071000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr9:108062400-108098800	Weak transcription	Spleen	Spleen
49	chr9:108062400-108104600	Weak transcription	Right Ventricle	heart
50	chr9:108062600-108063600	Strong transcription	Fetal Intestine Large	intestine

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