Variant report

Variant	rs1058569
Chromosome Location	chr3:28288500-28288501
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:28282357..28285690-chr3:28288463..28290366,3	MCF-7	breast:
2	chr3:28216893..28219408-chr3:28288300..28290033,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187118	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11129315	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11129316	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11926578	0.90[ASN][1000 genomes]
rs1609729	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680747	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680907	0.86[ASN][1000 genomes]
rs6551247	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[ASN][1000 genomes]
rs6551248	0.88[ASN][1000 genomes]
rs6551253	1.00[JPT][hapmap]
rs6789421	0.94[JPT][hapmap]
rs6791550	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6795783	0.93[EUR][1000 genomes]
rs7611318	0.96[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7612033	1.00[JPT][hapmap]
rs7613767	1.00[JPT][hapmap]
rs7621688	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9831010	0.94[JPT][hapmap]
rs996939	0.82[CHB][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	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer 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	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1058569	ENSG00000187118	cis	multi-tissue	Pritchard
rs1058569	EOMES	cis	cerebellum	SCAN
rs1058569	OXSM	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28283800-28311400	Weak transcription	Lung	lung
2	chr3:28284000-28290000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:28284000-28290800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:28284000-28304800	Weak transcription	Primary B cells from cord blood	blood
5	chr3:28284000-28309600	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:28284000-28313800	Weak transcription	Ovary	ovary
7	chr3:28284000-28317200	Weak transcription	Gastric	stomach
8	chr3:28284200-28288600	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:28284200-28288800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:28284200-28292600	Weak transcription	Psoas Muscle	Psoas
11	chr3:28284200-28292800	Weak transcription	Small Intestine	intestine
12	chr3:28284400-28288600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:28284400-28291400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:28284400-28292200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:28284400-28293600	Weak transcription	Right Ventricle	heart
16	chr3:28284400-28305400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:28284400-28305800	Weak transcription	Hela-S3	cervix
18	chr3:28284400-28311000	Weak transcription	Fetal Intestine Small	intestine
19	chr3:28284400-28312600	Weak transcription	Fetal Lung	lung
20	chr3:28284400-28321800	Weak transcription	NHLF	lung
21	chr3:28284600-28289400	Enhancers	Dnd41	blood
22	chr3:28284600-28291600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:28284600-28292200	Weak transcription	NHEK	skin
24	chr3:28284600-28292400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:28284600-28293400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:28284600-28305600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:28284600-28306000	Weak transcription	A549	lung
28	chr3:28284600-28307200	Weak transcription	Fetal Intestine Large	intestine
29	chr3:28284600-28311200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:28285200-28288800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr3:28285200-28305200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:28285200-28305600	Weak transcription	Fetal Thymus	thymus
33	chr3:28285400-28294000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:28285600-28290200	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr3:28285600-28315400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:28285800-28305400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:28285800-28311000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:28286000-28288600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr3:28286000-28288600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:28286000-28290200	Weak transcription	Placenta	Placenta
41	chr3:28286000-28292200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:28286000-28292600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:28286000-28294000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr3:28286000-28306000	Weak transcription	K562	blood
45	chr3:28286000-28307200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr3:28286200-28288800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:28286200-28291400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:28286200-28294400	Weak transcription	Spleen	Spleen
49	chr3:28286400-28288800	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr3:28286400-28291200	Weak transcription	Primary monocytes fromperipheralblood	blood

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