Variant report

Variant	rs17153415
Chromosome Location	chr11:58925860-58925861
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	chr11:58921112..58922649-chr11:58924123..58926292,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10128605	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10128661	0.91[EUR][1000 genomes]
rs10437720	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10792219	0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs10792221	0.87[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896914	0.85[EUR][1000 genomes]
rs10896922	0.89[EUR][1000 genomes]
rs10896924	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs10896925	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896926	0.90[EUR][1000 genomes]
rs10896928	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896929	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10896930	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10896931	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10896932	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10896933	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10896934	0.89[EUR][1000 genomes]
rs10896935	0.87[EUR][1000 genomes]
rs10896936	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10896937	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10896938	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229798	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs11229799	0.86[EUR][1000 genomes]
rs11229800	0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs11229801	0.87[EUR][1000 genomes]
rs11229837	0.92[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11229840	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229848	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229849	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229850	0.94[CEU][hapmap]
rs11229851	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11229852	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11229854	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11229856	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11823977	0.90[EUR][1000 genomes]
rs11825017	0.90[EUR][1000 genomes]
rs12271831	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12272113	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12274008	0.94[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12275487	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12278163	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12280068	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12283633	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12292185	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12293649	0.94[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12293695	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12362905	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12802129	0.90[EUR][1000 genomes]
rs17153379	0.90[EUR][1000 genomes]
rs17153383	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1938588	0.90[EUR][1000 genomes]
rs1938589	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1938781	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2096544	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2096586	0.91[EUR][1000 genomes]
rs2096587	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2105506	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2105507	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2154628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2186380	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2282482	0.89[EUR][1000 genomes]
rs2282483	0.88[EUR][1000 genomes]
rs2849739	0.81[EUR][1000 genomes]
rs34027305	0.90[EUR][1000 genomes]
rs34239454	0.86[EUR][1000 genomes]
rs34501069	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35293773	0.86[EUR][1000 genomes]
rs3802961	0.90[EUR][1000 genomes]
rs474847	0.87[EUR][1000 genomes]
rs55657403	0.90[EUR][1000 genomes]
rs55689653	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55989038	0.89[EUR][1000 genomes]
rs56137001	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56239606	0.89[EUR][1000 genomes]
rs58722008	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61902181	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61902223	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7126078	0.90[EUR][1000 genomes]
rs7933787	1.00[ASW][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];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7950880	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17153415	FAM111A	cis	parietal	SCAN
rs17153415	C11orf31	cis	parietal	SCAN
rs17153415	OR5AK2	cis	parietal	SCAN
rs17153415	CD5	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58924600-58926000	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr11:58924800-58926000	Enhancers	Primary B cells from cord blood	blood
3	chr11:58924800-58926400	Enhancers	Primary B cells from peripheral blood	blood
4	chr11:58925200-58926000	Enhancers	GM12878-XiMat	blood
5	chr11:58925400-58926000	Enhancers	Fetal Muscle Leg	muscle
6	chr11:58925400-58926000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr11:58925600-58926000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:58925600-58926000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:58925600-58926000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr11:58925600-58926000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
11	chr11:58925600-58926000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr11:58925600-58926000	Enhancers	Primary T cells from cord blood	blood
13	chr11:58925600-58926000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr11:58925600-58926000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:58925600-58926000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:58925600-58926000	Enhancers	Dnd41	blood
17	chr11:58925600-58926000	Enhancers	HMEC	breast
18	chr11:58925600-58926200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:58925600-58926200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:58925600-58926400	Enhancers	Adipose Nuclei	Adipose
21	chr11:58925800-58926000	Enhancers	H1 Cell Line	embryonic stem cell
22	chr11:58925800-58926000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr11:58925800-58926000	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr11:58925800-58926000	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr11:58925800-58926000	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr11:58925800-58926000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:58925800-58926000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:58925800-58926000	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr11:58925800-58926000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr11:58925800-58926000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr11:58925800-58926000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr11:58925800-58926000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr11:58925800-58926000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:58925800-58926000	Enhancers	Muscle Satellite Cultured Cells	--
35	chr11:58925800-58926000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:58925800-58926000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr11:58925800-58926000	Enhancers	Duodenum Mucosa	Duodenum
38	chr11:58925800-58926000	Flanking Active TSS	Fetal Kidney	kidney
39	chr11:58925800-58926000	Enhancers	Fetal Lung	lung
40	chr11:58925800-58926000	Enhancers	Fetal Thymus	thymus
41	chr11:58925800-58926000	Enhancers	Left Ventricle	heart
42	chr11:58925800-58926000	Enhancers	Ovary	ovary
43	chr11:58925800-58926000	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr11:58925800-58926000	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr11:58925800-58926000	Enhancers	HSMM	muscle
46	chr11:58925800-58926000	Flanking Active TSS	HUVEC	blood vessel
47	chr11:58925800-58926000	Flanking Active TSS	NHLF	lung
48	chr11:58925800-58926000	Flanking Active TSS	Osteobl	bone
49	chr11:58925800-58926200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:58925800-58926200	Enhancers	Primary T helper cells PMA-I stimulated	--

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