Variant report

Variant	rs1508653
Chromosome Location	chr5:35618552-35618553
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	chr5:35618439..35620989-chr5:35639383..35642500,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10472976	0.88[ASN][1000 genomes]
rs10941251	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs10941252	0.85[JPT][hapmap]
rs11951251	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11960006	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12188514	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs12513652	0.85[JPT][hapmap]
rs12514518	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs12515734	0.83[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12653412	0.82[AMR][1000 genomes]
rs12654422	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12656037	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12657378	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12657936	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12658117	0.82[AMR][1000 genomes]
rs12659209	0.82[AMR][1000 genomes]
rs1508650	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1508651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1508652	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1605678	0.88[ASN][1000 genomes]
rs16902377	0.85[JPT][hapmap]
rs1848442	0.88[ASN][1000 genomes]
rs1994928	0.88[ASN][1000 genomes]
rs2088068	0.88[ASN][1000 genomes]
rs4501318	0.86[AMR][1000 genomes]
rs4623125	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4703419	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55838092	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60285353	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62352974	0.82[AMR][1000 genomes]
rs62353010	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7702882	0.88[ASN][1000 genomes]
rs7720593	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs977519	0.85[JPT][hapmap]

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	nsv525477	chr5:35530905-35792990	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1508653	FYB	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35616800-35619400	Flanking Active TSS	Dnd41	blood
2	chr5:35617200-35618600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:35617200-35618600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:35617200-35618600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:35617200-35618600	Active TSS	Fetal Kidney	kidney
6	chr5:35617200-35618600	Active TSS	Monocytes-CD14+_RO01746	blood
7	chr5:35617200-35618800	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr5:35617200-35618800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:35617200-35618800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:35617200-35618800	Active TSS	A549	lung
11	chr5:35617200-35618800	Active TSS	HMEC	breast
12	chr5:35617200-35618800	Active TSS	NHDF-Ad	bronchial
13	chr5:35617400-35618600	Active TSS	H9 Cell Line	embryonic stem cell
14	chr5:35617400-35618600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:35617400-35618600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr5:35617400-35618600	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr5:35617400-35618600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:35617400-35618600	Active TSS	Fetal Brain Female	brain
19	chr5:35617400-35618600	Active TSS	Fetal Intestine Small	intestine
20	chr5:35617400-35618600	Flanking Active TSS	Fetal Thymus	thymus
21	chr5:35617400-35618600	Active TSS	Right Atrium	heart
22	chr5:35617400-35618600	Active TSS	Right Ventricle	heart
23	chr5:35617400-35618800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
24	chr5:35617400-35618800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr5:35617400-35618800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr5:35617400-35618800	Active TSS	Brain Anterior Caudate	brain
27	chr5:35617400-35618800	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr5:35617400-35618800	Active TSS	Colon Smooth Muscle	Colon
29	chr5:35617400-35618800	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr5:35617400-35618800	Active TSS	Fetal Intestine Large	intestine
31	chr5:35617400-35618800	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr5:35617400-35618800	Active TSS	Rectal Smooth Muscle	rectum
33	chr5:35617400-35619000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:35617400-35619000	Active TSS	NHEK	skin
35	chr5:35617400-35619200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:35617600-35618600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
37	chr5:35617600-35618600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:35617600-35618600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:35617600-35618600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr5:35617600-35618600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr5:35617600-35618600	Active TSS	Fetal Lung	lung
42	chr5:35617600-35618600	Active TSS	Fetal Stomach	stomach
43	chr5:35617600-35618600	Active TSS	Gastric	stomach
44	chr5:35617600-35618600	Active TSS	Lung	lung
45	chr5:35617600-35618600	Active TSS	Psoas Muscle	Psoas
46	chr5:35617600-35618600	Active TSS	HSMMtube	muscle
47	chr5:35617600-35618800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
48	chr5:35617600-35618800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr5:35617600-35618800	Active TSS	Aorta	Aorta
50	chr5:35617600-35618800	Active TSS	Brain Germinal Matrix	brain

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