Variant report

Variant	rs16929505
Chromosome Location	chr9:12776840-12776841
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: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	chr9:12776384..12777092-chr9:12988313..12988856,2	MCF-7	breast:
2	chr9:12716514..12718700-chr9:12776478..12778096,2	MCF-7	breast:
3	chr9:12775994..12778011-chr9:12786037..12787743,2	K562	blood:
4	chr9:12771458..12774120-chr9:12775878..12777874,2	K562	blood:
5	chr9:12776291..12778540-chr9:12858744..12861808,3	MCF-7	breast:
6	chr9:12774954..12777056-chr9:12883374..12886318,3	MCF-7	breast:
7	chr9:12774109..12791345-chr9:12812800..12822770,37	MCF-7	breast:
8	chr9:12773974..12784053-chr9:12813051..12820453,19	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000235448	Chromatin interaction
ENSG00000222658	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs16929507	0.86[YRI][hapmap]
rs16929519	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3750503	0.92[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759671	chr9:12235048-12784092	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1034393	chr9:12278703-12798236	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv869288	chr9:12286919-12816766	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1029415	chr9:12424340-12794623	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv540064	chr9:12424340-12794623	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv2758182	chr9:12621991-12784092	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1030835	chr9:12717405-12840928	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv892573	chr9:12730636-12874703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv892574	chr9:12754969-12918226	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12774600-12778000	Active TSS	NHDF-Ad	bronchial
2	chr9:12774800-12777000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:12774800-12777000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:12774800-12777000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr9:12774800-12777000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr9:12774800-12777000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:12774800-12777000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr9:12774800-12777000	Active TSS	Brain Substantia Nigra	brain
9	chr9:12774800-12777000	Active TSS	Left Ventricle	heart
10	chr9:12774800-12777000	Active TSS	Right Ventricle	heart
11	chr9:12774800-12777000	Active TSS	Stomach Mucosa	stomach
12	chr9:12774800-12777200	Active TSS	Psoas Muscle	Psoas
13	chr9:12774800-12777200	Active TSS	Osteobl	bone
14	chr9:12774800-12777400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:12774800-12777400	Active TSS	Brain Angular Gyrus	brain
16	chr9:12774800-12777400	Active TSS	Brain Anterior Caudate	brain
17	chr9:12774800-12777400	Active TSS	Brain Hippocampus Middle	brain
18	chr9:12774800-12777400	Active TSS	Fetal Muscle Trunk	muscle
19	chr9:12774800-12777400	Active TSS	Ovary	ovary
20	chr9:12774800-12777400	Active TSS	A549	lung
21	chr9:12774800-12777600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr9:12774800-12777600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr9:12774800-12777800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:12774800-12777800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:12774800-12778000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:12774800-12778000	Active TSS	Colon Smooth Muscle	Colon
27	chr9:12774800-12778000	Active TSS	Fetal Intestine Large	intestine
28	chr9:12774800-12778000	Active TSS	Rectal Smooth Muscle	rectum
29	chr9:12774800-12778000	Active TSS	NHEK	skin
30	chr9:12774800-12778200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:12774800-12778200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:12774800-12778200	Active TSS	Aorta	Aorta
33	chr9:12774800-12778200	Active TSS	Fetal Stomach	stomach
34	chr9:12774800-12778200	Active TSS	Right Atrium	heart
35	chr9:12774800-12778400	Active TSS	NHLF	lung
36	chr9:12774800-12779000	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr9:12774800-12779000	Active TSS	Stomach Smooth Muscle	stomach
38	chr9:12775000-12777000	Active TSS	Esophagus	oesophagus
39	chr9:12775000-12777000	Active TSS	Gastric	stomach
40	chr9:12775000-12777000	Active TSS	Pancreas	Pancrea
41	chr9:12775000-12777000	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr9:12775000-12777000	Bivalent/Poised TSS	Thymus	Thymus
43	chr9:12775000-12777200	Active TSS	Fetal Intestine Small	intestine
44	chr9:12775000-12777400	Active TSS	Colonic Mucosa	Colon
45	chr9:12775000-12777400	Active TSS	Lung	lung
46	chr9:12775000-12779200	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr9:12775200-12777000	Active TSS	Small Intestine	intestine
48	chr9:12775800-12777000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr9:12775800-12779000	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr9:12776000-12777000	Flanking Active TSS	HUVEC	blood vessel

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