Variant report

Variant	rs11038428
Chromosome Location	chr11:45404318-45404319
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:45402149..45405049-chr11:45410823..45413385,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10838464	0.85[EUR][1000 genomes]
rs10838465	0.85[EUR][1000 genomes]
rs10838467	0.84[EUR][1000 genomes]
rs12224037	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12271560	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12275086	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs1873056	0.83[EUR][1000 genomes]
rs2046733	0.84[EUR][1000 genomes]
rs34042421	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35072015	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59678781	0.84[EUR][1000 genomes]
rs7928480	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7943688	0.84[EUR][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	nsv530619	chr11:45294176-45553928	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv467869	chr11:45389225-45415035	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv554185	chr11:45389225-45415035	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11038428	LRP4	cis	parietal	SCAN
rs11038428	SYT13	cis	parietal	SCAN
rs11038428	MTCH2	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45393800-45406200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:45394200-45406200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:45396600-45404400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr11:45397400-45404600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr11:45403200-45405400	Enhancers	Ovary	ovary
6	chr11:45403200-45408400	Enhancers	Brain Germinal Matrix	brain
7	chr11:45403200-45410000	Enhancers	Fetal Thymus	thymus
8	chr11:45403400-45404800	Enhancers	Primary T cells fromperipheralblood	blood
9	chr11:45403400-45406000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr11:45403600-45405000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr11:45403600-45405400	Enhancers	Primary hematopoietic stem cells	blood
12	chr11:45403600-45405800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
13	chr11:45403600-45407800	Enhancers	Thymus	Thymus
14	chr11:45403600-45408000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr11:45403800-45404400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:45403800-45404800	Weak transcription	Lung	lung
17	chr11:45403800-45405200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr11:45403800-45405200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr11:45403800-45405400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:45403800-45405400	Enhancers	Osteobl	bone
21	chr11:45403800-45405600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr11:45403800-45405600	Enhancers	Primary T cells from cord blood	blood
23	chr11:45404000-45405000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:45404000-45406800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr11:45404200-45404800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr11:45404200-45405000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:45404200-45405000	Enhancers	Fetal Brain Female	brain
28	chr11:45404200-45405200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:45404200-45405200	Enhancers	Fetal Lung	lung
30	chr11:45404200-45405200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
31	chr11:45404200-45405400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr11:45404200-45405400	Enhancers	Muscle Satellite Cultured Cells	--
33	chr11:45404200-45405400	Enhancers	Right Atrium	heart
34	chr11:45404200-45405400	Enhancers	HSMM	muscle
35	chr11:45404200-45405400	Enhancers	HSMMtube	muscle
36	chr11:45404200-45407800	Enhancers	Fetal Brain Male	brain

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