Variant report

Variant	rs73644661
Chromosome Location	chr9:15553354-15553355
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15509318..15512022-chr9:15550389..15555494,9	MCF-7	breast:
2	chr3:5020895..5021614-chr9:15552897..15553484,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNAPC3-3	chr9:15553289-15553604	NONHSAT130275

Variant related genes	Relation type
ENSG00000134107	Chromatin interaction
ENSG00000164985	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11999047	0.83[AFR][1000 genomes]
rs11999354	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11999403	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12002030	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12002408	0.82[AFR][1000 genomes]
rs12003098	1.00[AMR][1000 genomes]
rs16933373	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16933376	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35546678	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55678381	1.00[AMR][1000 genomes]
rs56304941	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56333848	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56974853	1.00[AMR][1000 genomes]
rs57098037	1.00[AMR][1000 genomes]
rs57108331	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57201285	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57471536	0.90[AFR][1000 genomes]
rs57688272	1.00[AMR][1000 genomes]
rs58027597	0.90[AFR][1000 genomes]
rs58596549	1.00[AMR][1000 genomes]
rs58892201	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59228819	1.00[AMR][1000 genomes]
rs59254174	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59736306	1.00[AMR][1000 genomes]
rs60294159	1.00[AMR][1000 genomes]
rs60918672	1.00[AMR][1000 genomes]
rs61608504	1.00[AMR][1000 genomes]
rs7033545	0.85[AFR][1000 genomes]
rs73644680	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73644681	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73644683	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73644686	1.00[AMR][1000 genomes]
rs73644689	1.00[AMR][1000 genomes]
rs73644690	1.00[AMR][1000 genomes]
rs73644691	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73644692	1.00[AMR][1000 genomes]
rs73644693	1.00[AMR][1000 genomes]
rs73644695	1.00[AMR][1000 genomes]
rs7468160	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv892629	chr9:15516375-15634326	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3407839	chr9:15530438-15665653	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15551800-15553400	Active TSS	Fetal Muscle Trunk	muscle
2	chr9:15551800-15553800	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr9:15551800-15553800	Active TSS	Brain Cingulate Gyrus	brain
4	chr9:15551800-15554200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:15551800-15554400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:15551800-15554400	Active TSS	Brain Angular Gyrus	brain
7	chr9:15551800-15554400	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr9:15551800-15554400	Active TSS	Fetal Brain Female	brain
9	chr9:15551800-15554600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr9:15551800-15554600	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr9:15552000-15553400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:15552000-15553400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr9:15552000-15553400	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr9:15552000-15553400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr9:15552000-15553600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:15552000-15553600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:15552000-15553600	Active TSS	Primary T cells from cord blood	blood
18	chr9:15552000-15553600	Active TSS	Muscle Satellite Cultured Cells	--
19	chr9:15552000-15553600	Active TSS	Fetal Muscle Leg	muscle
20	chr9:15552000-15553600	Active TSS	HSMM	muscle
21	chr9:15552000-15553800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:15552000-15553800	Flanking Active TSS	Liver	Liver
23	chr9:15552000-15553800	Active TSS	Pancreas	Pancrea
24	chr9:15552000-15554000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr9:15552000-15554000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:15552000-15554000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:15552000-15554000	Active TSS	Brain Substantia Nigra	brain
28	chr9:15552000-15554000	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr9:15552000-15554000	Active TSS	Rectal Smooth Muscle	rectum
30	chr9:15552000-15554000	Active TSS	Right Atrium	heart
31	chr9:15552000-15554000	Active TSS	Stomach Smooth Muscle	stomach
32	chr9:15552000-15554000	Active TSS	HSMMtube	muscle
33	chr9:15552000-15554200	Active TSS	Brain Hippocampus Middle	brain
34	chr9:15552000-15554400	Active TSS	H9 Cell Line	embryonic stem cell
35	chr9:15552000-15554400	Active TSS	Thymus	Thymus
36	chr9:15552000-15554600	Active TSS	NHDF-Ad	bronchial
37	chr9:15552200-15553400	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr9:15552200-15553400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:15552200-15553400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr9:15552200-15553400	Active TSS	Fetal Intestine Small	intestine
41	chr9:15552200-15553400	Active TSS	NH-A	brain
42	chr9:15552200-15553600	Active TSS	Colon Smooth Muscle	Colon
43	chr9:15552200-15553600	Active TSS	Fetal Heart	heart
44	chr9:15552200-15553600	Active TSS	Fetal Lung	lung
45	chr9:15552200-15553600	Active TSS	Left Ventricle	heart
46	chr9:15552200-15553600	Active TSS	Hela-S3	cervix
47	chr9:15552200-15553800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:15552200-15553800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr9:15552200-15553800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr9:15552200-15553800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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