Variant report

Variant	rs2416306
Chromosome Location	chr5:112483932-112483933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112482887..112485655-chr5:112487737..112490349,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10068491	0.89[CHD][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10463646	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13168126	0.84[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs13190040	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1562016	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1947026	0.81[CHD][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs2044238	0.87[CEU][hapmap];0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2044239	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2165930	0.80[AMR][1000 genomes]
rs2165931	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2416303	0.86[CEU][hapmap];0.94[CHB][hapmap];0.83[EUR][1000 genomes]
rs2416305	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4705794	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4705795	0.90[CHB][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs4705796	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4705797	0.94[CHB][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes]
rs7707546	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7720549	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7720866	0.87[CEU][hapmap];0.89[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7726679	1.00[CHB][hapmap];0.87[MEX][hapmap]
rs935159	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2416306	MCC	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112467400-112493200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:112470200-112491000	Weak transcription	Fetal Kidney	kidney
3	chr5:112477200-112485400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:112477400-112486600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:112477400-112486600	Weak transcription	Right Atrium	heart
6	chr5:112477400-112489200	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:112477400-112500600	Weak transcription	Fetal Stomach	stomach
8	chr5:112478000-112485600	Weak transcription	Pancreas	Pancrea
9	chr5:112478000-112497000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr5:112479200-112485200	Weak transcription	Liver	Liver
11	chr5:112479200-112490000	Weak transcription	Aorta	Aorta
12	chr5:112479400-112489600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:112479800-112485600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:112480400-112487200	Weak transcription	Right Ventricle	heart
15	chr5:112481400-112496000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:112481600-112485400	Weak transcription	Ovary	ovary
17	chr5:112481800-112486400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:112481800-112487800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:112482000-112484200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr5:112482000-112484400	Enhancers	Fetal Heart	heart
21	chr5:112482600-112484000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:112482600-112491400	Weak transcription	Adipose Nuclei	Adipose
23	chr5:112482800-112484000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:112482800-112484400	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr5:112483000-112484000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr5:112483000-112484200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr5:112483000-112484200	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr5:112483000-112496800	Weak transcription	HMEC	breast
29	chr5:112483200-112484000	Enhancers	H9 Cell Line	embryonic stem cell
30	chr5:112483200-112495800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:112483400-112488800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:112483400-112489200	Weak transcription	NHLF	lung
33	chr5:112483400-112490000	Weak transcription	Left Ventricle	heart
34	chr5:112483400-112491800	Weak transcription	NHEK	skin
35	chr5:112483400-112494600	Weak transcription	Psoas Muscle	Psoas
36	chr5:112483600-112485200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:112483600-112485400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:112483600-112485400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:112483600-112485400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr5:112483600-112485600	Weak transcription	Osteobl	bone
41	chr5:112483600-112486400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:112483600-112486600	Weak transcription	Gastric	stomach
43	chr5:112483600-112488800	Weak transcription	NHDF-Ad	bronchial
44	chr5:112483600-112489200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:112483800-112484200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:112483800-112485400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr5:112483800-112485600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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