Variant report

Variant	rs9548819
Chromosome Location	chr13:40128303-40128304
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:40126439..40128826-chr13:40132731..40135327,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1885759	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2324337	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35396912	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7322336	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7333056	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7981547	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7982917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9315701	0.96[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9315702	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9315703	1.00[CEU][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9315706	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9315707	0.92[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs9532396	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9532399	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9548800	0.81[GIH][hapmap]
rs9548804	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9548805	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9548809	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9548817	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9548820	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548821	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548822	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9548824	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9548825	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9548826	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9548827	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9548829	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9548830	0.92[CEU][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs9548836	0.86[CHB][hapmap]
rs9603564	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv523936	chr13:40119410-40128845	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9548819	HLTF	trans	brain	seeQTL
rs9548819	FOXO1	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40107800-40140200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr13:40111200-40133200	Weak transcription	Aorta	Aorta
3	chr13:40111600-40128600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr13:40113800-40128600	Weak transcription	Ovary	ovary
5	chr13:40114000-40131200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr13:40114400-40136000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr13:40115400-40133200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr13:40115600-40133600	Weak transcription	Osteobl	bone
9	chr13:40117000-40130000	Weak transcription	Fetal Muscle Leg	muscle
10	chr13:40117000-40130400	Weak transcription	HSMMtube	muscle
11	chr13:40117800-40128600	Weak transcription	Right Atrium	heart
12	chr13:40117800-40131200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr13:40119800-40130200	Weak transcription	Fetal Heart	heart
14	chr13:40120000-40131600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr13:40121400-40136200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr13:40123000-40131800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr13:40123200-40128600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr13:40123200-40128600	Weak transcription	HMEC	breast
19	chr13:40125000-40131600	Weak transcription	Fetal Lung	lung
20	chr13:40125400-40133400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr13:40125600-40131400	Weak transcription	HSMM	muscle
22	chr13:40125600-40133000	Weak transcription	Lung	lung
23	chr13:40125800-40130000	Weak transcription	Adipose Nuclei	Adipose
24	chr13:40126000-40128800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr13:40126400-40128800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr13:40126400-40137200	Weak transcription	NHLF	lung
27	chr13:40126600-40130200	Weak transcription	Right Ventricle	heart
28	chr13:40126800-40130600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr13:40127000-40128800	Weak transcription	Brain Substantia Nigra	brain
30	chr13:40127000-40131200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr13:40127000-40133400	Weak transcription	Brain Angular Gyrus	brain
32	chr13:40127000-40136200	Weak transcription	NHDF-Ad	bronchial
33	chr13:40127200-40129000	Enhancers	Left Ventricle	heart
34	chr13:40128200-40128400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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