Variant report

Variant	rs12339837
Chromosome Location	chr9:7163316-7163317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10976076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10976077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10976082	1.00[MEX][hapmap]
rs12343417	1.00[AFR][1000 genomes]
rs12343985	0.82[YRI][hapmap];1.00[AFR][1000 genomes]
rs13440014	1.00[AFR][1000 genomes]
rs57689330	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv613259	chr9:7032776-7541338	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers 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	4 gene(s)	inside rSNPs	diseases
4	nsv1015874	chr9:7048807-7434890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv539971	chr9:7048807-7434890	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv892190	chr9:7094860-7186074	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv892191	chr9:7150997-7173752	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv892192	chr9:7153009-7257340	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7135200-7164800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr9:7147200-7171000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:7147400-7165600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:7147400-7174600	Weak transcription	NHEK	skin
5	chr9:7147800-7165200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:7148600-7172200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:7148600-7185400	Weak transcription	HMEC	breast
8	chr9:7148800-7164800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:7149000-7165000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:7149000-7165200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr9:7149200-7164800	Weak transcription	Liver	Liver
12	chr9:7149200-7165200	Weak transcription	Thymus	Thymus
13	chr9:7149400-7164600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr9:7149400-7165200	Weak transcription	Adipose Nuclei	Adipose
15	chr9:7149600-7172200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:7149600-7185400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr9:7149600-7186200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:7149800-7172800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr9:7150400-7175800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr9:7150600-7165200	Weak transcription	GM12878-XiMat	blood
21	chr9:7150800-7164600	Weak transcription	Fetal Thymus	thymus
22	chr9:7150800-7164800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr9:7150800-7165000	Weak transcription	Esophagus	oesophagus
24	chr9:7150800-7165200	Weak transcription	Spleen	Spleen
25	chr9:7150800-7165400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr9:7150800-7169400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr9:7150800-7172800	Weak transcription	Fetal Muscle Leg	muscle
28	chr9:7151200-7164400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr9:7151200-7165000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr9:7151200-7171000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr9:7151200-7173000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr9:7151400-7165000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr9:7151400-7165000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr9:7151400-7165000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr9:7151600-7163800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr9:7151600-7164000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr9:7151600-7164400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr9:7151600-7164400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr9:7151800-7164600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr9:7151800-7165000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr9:7151800-7188600	Weak transcription	Colonic Mucosa	Colon
42	chr9:7152000-7164000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr9:7152000-7165400	Weak transcription	Placenta	Placenta
44	chr9:7152000-7172600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr9:7154000-7165200	Weak transcription	Brain Hippocampus Middle	brain
46	chr9:7154000-7165600	Weak transcription	Brain Substantia Nigra	brain
47	chr9:7154200-7165200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr9:7154400-7164400	Weak transcription	HepG2	liver
49	chr9:7154400-7165000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr9:7154400-7165200	Weak transcription	Fetal Intestine Large	intestine

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