Variant report

Variant	rs9568558
Chromosome Location	chr13:51810953-51810954
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	chr13:51792474..51795123-chr13:51810834..51812856,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10492520	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs12427834	1.00[ASW][hapmap]
rs12427843	1.00[ASW][hapmap]
rs12584566	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs2148527	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2408301	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9563039	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9568554	0.87[AMR][1000 genomes]
rs9568557	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv832610	chr13:51636661-51822106	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832611	chr13:51766472-51938314	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9568558	EGFL6	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51799800-51818200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr13:51805200-51825600	Weak transcription	Aorta	Aorta
3	chr13:51806200-51814000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr13:51808000-51812600	Enhancers	Brain Cingulate Gyrus	brain
5	chr13:51808000-51821200	Enhancers	Brain Substantia Nigra	brain
6	chr13:51808400-51814400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr13:51808400-51821400	Enhancers	Fetal Heart	heart
8	chr13:51808600-51820000	Weak transcription	Fetal Brain Female	brain
9	chr13:51808800-51814000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr13:51808800-51816400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr13:51809000-51818200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr13:51809800-51813200	Enhancers	Fetal Lung	lung
13	chr13:51810000-51811400	Enhancers	Brain Angular Gyrus	brain
14	chr13:51810000-51818200	Weak transcription	Brain Germinal Matrix	brain
15	chr13:51810200-51811600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr13:51810200-51814000	Weak transcription	Colon Smooth Muscle	Colon
17	chr13:51810200-51814800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr13:51810200-51818200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr13:51810200-51820200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr13:51810400-51811000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr13:51810400-51811000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr13:51810400-51811600	Weak transcription	Left Ventricle	heart
23	chr13:51810400-51811600	Weak transcription	Right Atrium	heart
24	chr13:51810400-51811600	Weak transcription	Right Ventricle	heart
25	chr13:51810400-51812000	Weak transcription	Lung	lung
26	chr13:51810400-51812000	Weak transcription	Spleen	Spleen
27	chr13:51810400-51813400	Enhancers	Brain Hippocampus Middle	brain
28	chr13:51810400-51813400	Weak transcription	HUVEC	blood vessel
29	chr13:51810400-51814400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr13:51810400-51814400	Weak transcription	Fetal Stomach	stomach
31	chr13:51810400-51814600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr13:51810400-51816400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr13:51810400-51818000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr13:51810400-51820000	Weak transcription	Fetal Brain Male	brain
35	chr13:51810600-51811400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr13:51810600-51811600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr13:51810600-51812800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr13:51810600-51814200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr13:51810600-51814200	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr13:51810600-51814200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr13:51810600-51814200	Weak transcription	Brain Anterior Caudate	brain
42	chr13:51810600-51815000	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr13:51810600-51815000	Weak transcription	Adipose Nuclei	Adipose
44	chr13:51810600-51818200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr13:51810800-51812200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr13:51810800-51814600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr13:51810800-51814600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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