Variant report

Variant	rs299206
Chromosome Location	chr5:118323544-118323545
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:118323277..118326022-chr5:118603985..118605806,3	MCF-7	breast:
2	chr14:39581660..39583614-chr5:118323067..118325473,2	MCF-7	breast:
3	chr5:118322493..118325395-chr5:118402550..118406560,4	K562	blood:
4	chr5:118322938..118326606-chr5:118602920..118605792,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249494	Chromatin interaction
ENSG00000145779	Chromatin interaction
ENSG00000239011	Chromatin interaction
ENSG00000092208	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11241493	1.00[JPT][hapmap]
rs13170553	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs169917	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs213434	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2442123	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs299194	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs299201	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs299202	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs299205	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs299208	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs299209	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299214	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs368569	0.82[EUR][1000 genomes]
rs411110	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv882767	chr5:117931730-118385691	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1017548	chr5:118276479-118358394	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1015878	chr5:118288904-118414706	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537881	chr5:118288904-118414706	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118316200-118323800	Weak transcription	Gastric	stomach
2	chr5:118320000-118323800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:118322400-118323600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:118322400-118324800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:118322800-118323600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr5:118322800-118323600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr5:118322800-118324400	Active TSS	Fetal Muscle Leg	muscle
8	chr5:118323000-118323600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr5:118323000-118323600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr5:118323000-118323600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr5:118323000-118323600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:118323000-118323600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:118323000-118323600	Flanking Active TSS	Liver	Liver
14	chr5:118323000-118323600	Flanking Active TSS	Brain Angular Gyrus	brain
15	chr5:118323000-118323600	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr5:118323000-118323600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr5:118323000-118323600	Flanking Active TSS	Hela-S3	cervix
18	chr5:118323000-118323800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:118323000-118323800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:118323000-118323800	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr5:118323000-118323800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr5:118323000-118323800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:118323000-118323800	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr5:118323000-118323800	Flanking Active TSS	Brain Cingulate Gyrus	brain
25	chr5:118323000-118323800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr5:118323000-118323800	Flanking Active TSS	Fetal Kidney	kidney
27	chr5:118323000-118323800	Active TSS	Right Atrium	heart
28	chr5:118323000-118323800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr5:118323000-118323800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr5:118323000-118323800	Flanking Active TSS	Dnd41	blood
31	chr5:118323000-118324200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:118323000-118324800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr5:118323000-118324800	Active TSS	Right Ventricle	heart
34	chr5:118323000-118325000	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr5:118323000-118325000	Active TSS	NH-A	brain
36	chr5:118323200-118323600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr5:118323200-118323600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr5:118323200-118323600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:118323200-118323600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr5:118323200-118323600	Flanking Active TSS	Fetal Heart	heart
41	chr5:118323200-118323600	Flanking Active TSS	Fetal Intestine Large	intestine
42	chr5:118323200-118323600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr5:118323200-118323600	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr5:118323200-118323600	Flanking Active TSS	Stomach Mucosa	stomach
45	chr5:118323200-118323600	Flanking Active TSS	HepG2	liver
46	chr5:118323200-118323600	Enhancers	NHDF-Ad	bronchial
47	chr5:118323200-118323800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr5:118323200-118323800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr5:118323200-118323800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr5:118323200-118323800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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