Variant report

Variant	rs11740989
Chromosome Location	chr5:147160125-147160126
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:147158425..147160468-chr5:147160831..147162494,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176049	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11739071	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11745685	0.83[ASN][1000 genomes]
rs11746607	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12655202	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12657336	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17717032	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57882722	0.84[ASN][1000 genomes]
rs61500793	0.84[ASN][1000 genomes]
rs6873493	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021356	chr5:147103627-147310531	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1033907	chr5:147109014-147309076	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv537916	chr5:147109014-147309076	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147146800-147160600	Weak transcription	Primary T cells from cord blood	blood
2	chr5:147151400-147160600	Weak transcription	Fetal Lung	lung
3	chr5:147156000-147161400	Weak transcription	Primary B cells from cord blood	blood
4	chr5:147156200-147161200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr5:147158200-147160400	Enhancers	Brain Substantia Nigra	brain
6	chr5:147158600-147160200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:147158800-147160200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:147159200-147160400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr5:147159200-147160600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr5:147159200-147161600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:147159400-147160200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:147159400-147160200	Enhancers	Primary hematopoietic stem cells	blood
13	chr5:147159400-147160200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:147159400-147160200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:147159400-147160200	Flanking Active TSS	Fetal Brain Male	brain
16	chr5:147159400-147160600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr5:147159400-147162800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:147159600-147160200	Enhancers	Thymus	Thymus
19	chr5:147159600-147160400	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr5:147159600-147160400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
21	chr5:147159600-147160600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr5:147159600-147160800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr5:147159600-147161600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr5:147159600-147161600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr5:147159600-147162200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
26	chr5:147159600-147162800	Active TSS	Brain Hippocampus Middle	brain
27	chr5:147159800-147160200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:147159800-147160200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:147159800-147160200	Weak transcription	Fetal Thymus	thymus
30	chr5:147159800-147160400	Enhancers	Fetal Stomach	stomach
31	chr5:147159800-147160600	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr5:147159800-147161400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr5:147159800-147162400	Active TSS	H1 Cell Line	embryonic stem cell
34	chr5:147159800-147162600	Active TSS	Brain Germinal Matrix	brain
35	chr5:147159800-147162800	Active TSS	Fetal Brain Female	brain
36	chr5:147160000-147160200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:147160000-147160200	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr5:147160000-147160200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:147160000-147160400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:147160000-147160400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr5:147160000-147160400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:147160000-147160400	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr5:147160000-147162600	Active TSS	Brain Angular Gyrus	brain
44	chr5:147160000-147162800	Active TSS	Pancreatic Islets	Pancreatic Islet

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