Variant report

Variant	rs11054385
Chromosome Location	chr12:11776232-11776233
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	chr12:11774248..11776994-chr12:11784131..11786795,2	K562	blood:
2	chr12:11775387..11777781-chr12:11801742..11803423,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139083	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10772491	0.88[EUR][1000 genomes]
rs10772492	0.87[EUR][1000 genomes]
rs10845389	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10845390	0.92[EUR][1000 genomes]
rs10845391	0.92[EUR][1000 genomes]
rs10845394	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845396	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10845397	0.94[CEU][hapmap];0.88[CHB][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11054377	0.91[EUR][1000 genomes]
rs11054378	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11054379	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11054384	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054389	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054390	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11833870	0.91[EUR][1000 genomes]
rs11835584	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12366449	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368746	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371924	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763712	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs58419583	0.92[EUR][1000 genomes]
rs58572989	0.92[EUR][1000 genomes]
rs60345208	0.92[EUR][1000 genomes]
rs6488434	0.92[EUR][1000 genomes]
rs6488436	0.80[EUR][1000 genomes]
rs6488437	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488440	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132693	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133901	0.91[EUR][1000 genomes]
rs7311752	0.94[CEU][hapmap];0.88[CHB][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7313110	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7962768	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9668837	0.92[EUR][1000 genomes]
rs9669330	0.91[EUR][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	nsv898803	chr12:11757867-11794636	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv470267	chr12:11767406-11787989	Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11054385	M6PR	cis	cerebellum	SCAN
rs11054385	EMP1	cis	parietal	SCAN
rs11054385	KIAA1467	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11774400-11777000	Enhancers	Fetal Thymus	thymus
2	chr12:11774800-11776800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr12:11774800-11777000	Enhancers	H9 Cell Line	embryonic stem cell
4	chr12:11774800-11777000	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr12:11774800-11777200	Enhancers	Primary hematopoietic stem cells	blood
6	chr12:11775000-11776800	Enhancers	Thymus	Thymus
7	chr12:11775000-11777200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr12:11775200-11776800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr12:11775200-11777200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr12:11775200-11777200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr12:11775200-11777200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr12:11775400-11776600	Enhancers	H1 Cell Line	embryonic stem cell
13	chr12:11775400-11776800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:11775400-11776800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:11775400-11776800	Enhancers	HepG2	liver
16	chr12:11775400-11777000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr12:11775400-11777000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:11775400-11777200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:11775400-11777200	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr12:11775400-11777200	Enhancers	Liver	Liver
21	chr12:11775400-11777200	Enhancers	Fetal Lung	lung
22	chr12:11775400-11777200	Enhancers	Placenta Amnion	Placenta Amnion
23	chr12:11775400-11777200	Enhancers	GM12878-XiMat	blood
24	chr12:11775600-11776600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:11775600-11776600	Enhancers	Stomach Smooth Muscle	stomach
26	chr12:11775800-11776600	Enhancers	Placenta	Placenta
27	chr12:11776000-11776400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:11776000-11776400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr12:11776000-11776600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:11776000-11776600	Enhancers	Gastric	stomach
31	chr12:11776000-11776800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:11776000-11776800	Enhancers	K562	blood
33	chr12:11776000-11777000	Enhancers	Primary B cells from cord blood	blood
34	chr12:11776000-11777000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:11776000-11777200	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr12:11776000-11777200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr12:11776200-11776400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:11776200-11776800	Enhancers	NHEK	skin
39	chr12:11776200-11776800	Enhancers	Osteobl	bone

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