Variant report

Variant	rs11739315
Chromosome Location	chr5:98277192-98277193
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr5:98277160-98277495	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr5:98277012-98277476	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr5:98277003-98278079	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr5:98277185-98277402	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr5:98276996-98277495	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr5:98277187-98277495	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr5:98277191-98277391	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr5:98275181-98279858	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr5:98277186-98277443	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr5:98277041-98277434	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:98272097..98275128-chr5:98275593..98280478,6	MCF-7	breast:
2	chr5:98276533..98278644-chr5:98288923..98290589,2	K562	blood:
3	chr5:98269604..98273895-chr5:98275576..98277950,6	K562	blood:
4	chr5:98275762..98278033-chr5:98288005..98290423,2	K562	blood:
5	chr5:98276177..98277799-chr5:98286832..98289590,2	MCF-7	breast:
6	chr5:98261788..98268544-chr5:98272174..98280784,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200351	TF binding region
ENSG00000200351	Chromatin interaction
ENSG00000241597	Chromatin interaction
ENSG00000248489	Chromatin interaction
ENSG00000153922	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1126253	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11738445	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2302983	0.81[CHB][hapmap]
rs60421587	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62367700	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62367705	0.91[EUR][1000 genomes]
rs7702352	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7721369	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7725230	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9790858	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[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	nsv882415	chr5:98134186-98312447	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv882416	chr5:98146106-98312447	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv537818	chr5:98241627-98279192	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv537819	chr5:98253348-98299646	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98266200-98283600	Weak transcription	Colonic Mucosa	Colon
2	chr5:98266600-98291400	Weak transcription	Brain Germinal Matrix	brain
3	chr5:98266800-98278400	Weak transcription	Hela-S3	cervix
4	chr5:98266800-98283200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr5:98267400-98277800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:98272200-98277600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:98272400-98278000	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr5:98272600-98277200	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr5:98272600-98278600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr5:98272800-98277400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:98273600-98277800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr5:98274000-98277200	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr5:98274600-98280000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr5:98274800-98277400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr5:98274800-98278800	Weak transcription	HepG2	liver
16	chr5:98274800-98282800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:98274800-98297200	Weak transcription	Thymus	Thymus
18	chr5:98275400-98277200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr5:98275600-98277200	Enhancers	NHDF-Ad	bronchial
20	chr5:98275800-98277200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:98275800-98277200	Enhancers	Brain Anterior Caudate	brain
22	chr5:98275800-98277400	Enhancers	Brain Substantia Nigra	brain
23	chr5:98275800-98277600	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr5:98275800-98277800	Enhancers	Colon Smooth Muscle	Colon
25	chr5:98276000-98277200	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr5:98276000-98277200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:98276000-98277200	Enhancers	Adipose Nuclei	Adipose
28	chr5:98276000-98277200	Enhancers	Fetal Lung	lung
29	chr5:98276000-98277200	Enhancers	Osteobl	bone
30	chr5:98276000-98278000	Enhancers	Fetal Muscle Leg	muscle
31	chr5:98276000-98278600	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr5:98276200-98277200	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr5:98276200-98277200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:98276200-98277200	Enhancers	Fetal Heart	heart
35	chr5:98276200-98277200	Enhancers	Psoas Muscle	Psoas
36	chr5:98276200-98277200	Enhancers	HSMMtube	muscle
37	chr5:98276200-98277200	Enhancers	NHLF	lung
38	chr5:98276200-98277400	Enhancers	Brain Angular Gyrus	brain
39	chr5:98276200-98277400	Enhancers	Brain Hippocampus Middle	brain
40	chr5:98276200-98277400	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr5:98276200-98277600	Enhancers	Stomach Smooth Muscle	stomach
42	chr5:98276200-98278200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:98276200-98278800	Enhancers	Primary B cells from cord blood	blood
44	chr5:98276200-98281600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:98276400-98277200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:98276400-98277200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr5:98276400-98277200	Enhancers	Small Intestine	intestine
48	chr5:98276400-98277400	Enhancers	Ovary	ovary
49	chr5:98276400-98277600	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr5:98276400-98277600	Enhancers	Left Ventricle	heart

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