Variant report

Variant	rs12380362
Chromosome Location	chr9:16521534-16521535
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	chr9:16520489..16522214-chr9:16551948..16553682,2	MCF-7	breast:
2	chr9:16519927..16521803-chr9:16525394..16528325,2	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10756758	0.90[JPT][hapmap]
rs10756760	0.95[CEU][hapmap]
rs12377857	0.89[EUR][1000 genomes]
rs16934784	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs16934786	0.85[MKK][hapmap]
rs1927631	0.90[CEU][hapmap];0.86[GIH][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv892647	chr9:16476144-16521534	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1028923	chr9:16519711-16547863	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12380362	SLC24A2	cis	parietal	SCAN
rs12380362	TTC39B	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16515600-16522000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr9:16515600-16532600	Weak transcription	Aorta	Aorta
3	chr9:16516200-16521600	Weak transcription	HSMMtube	muscle
4	chr9:16516200-16521800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr9:16516200-16522000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr9:16516200-16522000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:16516200-16522000	Weak transcription	Left Ventricle	heart
8	chr9:16516200-16522200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:16516200-16524800	Weak transcription	Lung	lung
10	chr9:16517000-16522000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr9:16517200-16522000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:16517200-16522000	Weak transcription	Fetal Thymus	thymus
13	chr9:16517200-16522000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr9:16517200-16526800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr9:16517600-16521600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr9:16517600-16521800	Weak transcription	Fetal Kidney	kidney
17	chr9:16518000-16521600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:16518000-16524200	Weak transcription	A549	lung
19	chr9:16518400-16521800	Weak transcription	HUVEC	blood vessel
20	chr9:16518800-16524800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:16519000-16523200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:16519400-16522400	Enhancers	Fetal Lung	lung
23	chr9:16519600-16522000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:16519600-16525000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:16520000-16521800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr9:16520000-16522000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr9:16520000-16522200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr9:16520000-16522400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:16520000-16522400	Enhancers	NHDF-Ad	bronchial
30	chr9:16520000-16523200	Enhancers	Fetal Stomach	stomach
31	chr9:16520000-16524200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:16520200-16522000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr9:16520200-16522000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr9:16520200-16522000	Weak transcription	Psoas Muscle	Psoas
35	chr9:16520200-16522200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr9:16520200-16522200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr9:16520200-16523000	Enhancers	HMEC	breast
38	chr9:16520200-16523200	Enhancers	NHLF	lung
39	chr9:16520200-16524000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr9:16520200-16535400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:16520400-16522000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:16520400-16522200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr9:16520400-16523200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:16520400-16523200	Enhancers	Osteobl	bone
45	chr9:16520600-16522000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr9:16520600-16522800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr9:16520600-16525200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:16520800-16522200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr9:16520800-16523000	Enhancers	Colon Smooth Muscle	Colon
50	chr9:16521000-16522000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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