Variant report

Variant	rs4352559
Chromosome Location	chr5:60586625-60586626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:60586340..60593423-chr5:60595007..60600646,11	MCF-7	breast:
2	chr5:60584158..60587247-chr5:60624998..60628232,3	MCF-7	breast:
3	chr5:60580863..60583742-chr5:60584311..60586835,2	MCF-7	breast:
4	chr5:60586331..60590191-chr5:60626187..60629992,4	MCF-7	breast:
5	chr5:60581805..60584600-chr5:60585174..60586685,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130449	Chromatin interaction

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

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

rs_ID	r²[population]
rs12523278	0.82[TSI][hapmap]
rs4132385	0.80[EUR][1000 genomes]
rs4391122	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs4546329	0.96[CEU][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs4583848	0.85[EUR][1000 genomes]
rs4604142	0.81[CEU][hapmap];0.80[MEX][hapmap]
rs4700418	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs6449528	0.80[ASW][hapmap];0.81[CEU][hapmap]
rs7701440	0.81[CEU][hapmap];0.80[MEX][hapmap]
rs7724551	0.81[CEU][hapmap];0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60573400-60594800	Weak transcription	Right Atrium	heart
2	chr5:60576600-60588800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:60583600-60587000	Weak transcription	Colonic Mucosa	Colon
4	chr5:60583800-60587200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:60583800-60588200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:60584400-60587200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr5:60584600-60587000	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr5:60584800-60587000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr5:60585000-60587200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:60585200-60586800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr5:60585200-60587200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:60585200-60587400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:60585200-60587400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr5:60585200-60587400	Enhancers	Placenta	Placenta
15	chr5:60585400-60587400	Enhancers	Fetal Lung	lung
16	chr5:60585400-60587600	Enhancers	NHLF	lung
17	chr5:60585400-60589400	Enhancers	Pancreas	Pancrea
18	chr5:60585600-60587400	Enhancers	Hela-S3	cervix
19	chr5:60585600-60588800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:60585800-60586800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:60585800-60587000	Enhancers	Rectal Smooth Muscle	rectum
22	chr5:60585800-60587000	Enhancers	Small Intestine	intestine
23	chr5:60585800-60587200	Enhancers	Brain Substantia Nigra	brain
24	chr5:60585800-60588400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:60585800-60588800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr5:60586000-60586800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:60586000-60586800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:60586000-60588800	Weak transcription	Lung	lung
29	chr5:60586200-60587000	Enhancers	Liver	Liver
30	chr5:60586400-60586800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr5:60586400-60587000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:60586400-60587200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr5:60586400-60587200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:60586400-60587400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr5:60586400-60587400	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr5:60586400-60588200	Enhancers	Fetal Kidney	kidney
37	chr5:60586400-60589600	Enhancers	Stomach Mucosa	stomach
38	chr5:60586600-60586800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:60586600-60586800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr5:60586600-60586800	Enhancers	Esophagus	oesophagus
41	chr5:60586600-60586800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr5:60586600-60586800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr5:60586600-60586800	Enhancers	Spleen	Spleen
44	chr5:60586600-60586800	Genic enhancers	HSMM	muscle
45	chr5:60586600-60586800	Enhancers	HUVEC	blood vessel
46	chr5:60586600-60587000	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr5:60586600-60587000	Enhancers	H9 Cell Line	embryonic stem cell
48	chr5:60586600-60587000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:60586600-60587000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:60586600-60587000	Enhancers	Fetal Stomach	stomach

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