Variant report

Variant	rs2416315
Chromosome Location	chr5:112530417-112530418
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	chr5:112529246..112531364-chr5:112539078..112541052,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1007172	0.83[CEU][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10072487	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11739347	0.84[JPT][hapmap]
rs11955699	0.83[CEU][hapmap]
rs13156236	0.83[CEU][hapmap]
rs1443685	0.83[CEU][hapmap]
rs1443687	0.83[CEU][hapmap]
rs2416313	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs2416314	0.84[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes]
rs2900071	0.88[AMR][1000 genomes]
rs4705547	0.83[CEU][hapmap]
rs4705801	0.80[CEU][hapmap];0.95[JPT][hapmap]
rs4705802	0.80[LWK][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap]
rs6859190	1.00[CEU][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6876116	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6896522	0.83[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7719681	0.89[JPT][hapmap]
rs7720516	0.83[CEU][hapmap]
rs935162	0.83[CEU][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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112514400-112530600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr5:112515800-112538000	Weak transcription	Fetal Kidney	kidney
3	chr5:112518600-112538600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:112522000-112538800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:112522600-112530600	Weak transcription	Adipose Nuclei	Adipose
6	chr5:112522600-112534800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:112522600-112535200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:112522600-112535200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:112522600-112541000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:112522800-112535000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:112524800-112531200	Weak transcription	Brain Substantia Nigra	brain
12	chr5:112524800-112531800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:112525800-112530600	Weak transcription	Right Ventricle	heart
14	chr5:112525800-112533400	Weak transcription	Spleen	Spleen
15	chr5:112526400-112535000	Weak transcription	NH-A	brain
16	chr5:112526600-112531000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:112526600-112535000	Weak transcription	NHDF-Ad	bronchial
18	chr5:112526600-112535200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr5:112526800-112530600	Weak transcription	Lung	lung
20	chr5:112526800-112535000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:112526800-112535000	Weak transcription	HMEC	breast
22	chr5:112527400-112530800	Weak transcription	NHEK	skin
23	chr5:112527400-112538800	Weak transcription	Esophagus	oesophagus
24	chr5:112527800-112530600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:112527800-112533800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:112528600-112538600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr5:112529000-112531400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:112529000-112532200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:112529000-112538800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:112529200-112530600	Weak transcription	Fetal Lung	lung
31	chr5:112529200-112533600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:112529400-112531200	Enhancers	Liver	Liver
33	chr5:112529400-112532000	Enhancers	Fetal Heart	heart
34	chr5:112529400-112535000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr5:112529600-112535000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr5:112529800-112532200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:112530000-112531400	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr5:112530000-112531600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr5:112530000-112532200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:112530200-112530600	Weak transcription	Fetal Muscle Leg	muscle
41	chr5:112530200-112530800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:112530200-112531000	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr5:112530200-112532000	Enhancers	Left Ventricle	heart
44	chr5:112530200-112532200	Enhancers	Ovary	ovary
45	chr5:112530200-112532600	Enhancers	Psoas Muscle	Psoas
46	chr5:112530200-112538800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr5:112530400-112530800	Weak transcription	Aorta	Aorta
48	chr5:112530400-112534000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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