Variant report

Variant	rs3748164
Chromosome Location	chr9:117880357-117880358
allele	G/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:11)

rs_ID	r²[population]
rs12343517	0.81[ASN][1000 genomes]
rs12683537	0.99[ASN][1000 genomes]
rs12685855	0.96[ASN][1000 genomes]
rs1335346	0.80[ASN][1000 genomes]
rs3748165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56883831	0.96[ASN][1000 genomes]
rs57178492	0.99[ASN][1000 genomes]
rs57245991	0.99[ASN][1000 genomes]
rs57262272	0.96[ASN][1000 genomes]
rs57654109	0.92[ASN][1000 genomes]
rs59797450	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117877200-117881400	Active TSS	Fetal Kidney	kidney
2	chr9:117877600-117881600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
3	chr9:117878000-117881600	Active TSS	Colon Smooth Muscle	Colon
4	chr9:117878200-117880400	Active TSS	Rectal Smooth Muscle	rectum
5	chr9:117878200-117880800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr9:117878200-117881000	Active TSS	NHLF	lung
7	chr9:117878200-117881400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:117878200-117881600	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr9:117878200-117881600	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr9:117878400-117880600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:117878400-117881000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:117878600-117880400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr9:117878600-117880600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
14	chr9:117878600-117880600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
15	chr9:117878600-117881400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:117878600-117881400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:117878800-117880800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr9:117879000-117881400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr9:117879000-117881400	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr9:117879200-117880800	Active TSS	NHDF-Ad	bronchial
21	chr9:117879200-117881000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
22	chr9:117879200-117881000	Active TSS	Esophagus	oesophagus
23	chr9:117879400-117880400	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr9:117879400-117880800	Active TSS	NH-A	brain
25	chr9:117879600-117880600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:117879600-117881200	Flanking Active TSS	Fetal Lung	lung
27	chr9:117879800-117880600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:117879800-117880600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:117879800-117880600	Bivalent/Poised TSS	Fetal Thymus	thymus
30	chr9:117879800-117880600	Active TSS	NHEK	skin
31	chr9:117879800-117880800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:117879800-117880800	Active TSS	Osteobl	bone
33	chr9:117879800-117881200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
34	chr9:117879800-117881200	Active TSS	Brain Substantia Nigra	brain
35	chr9:117879800-117881400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr9:117879800-117881800	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr9:117879800-117881800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr9:117880000-117880400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr9:117880000-117880600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:117880000-117880800	Bivalent/Poised TSS	Fetal Brain Female	brain
41	chr9:117880000-117881000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:117880000-117881000	Bivalent Enhancer	Fetal Heart	heart
43	chr9:117880000-117881200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
44	chr9:117880000-117881400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr9:117880200-117880400	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:117880200-117880400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:117880200-117880400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr9:117880200-117880400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr9:117880200-117880400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr9:117880200-117880400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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