Variant report

Variant	rs2658547
Chromosome Location	chr11:18528815-18528816
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18527234..18530120-chr11:18547134..18549808,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000074319	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10219146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12283473	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16935424	1.00[JPT][hapmap]
rs16935432	1.00[JPT][hapmap]
rs16935557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17392588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1857909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1973412	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2056781	1.00[JPT][hapmap]
rs2271079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2643868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2896526	1.00[JPT][hapmap]
rs35593189	1.00[JPT][hapmap]
rs3740713	1.00[JPT][hapmap]
rs72871724	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72871727	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72871772	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72876735	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72876768	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72876784	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv1038015	chr11:18435855-18558211	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	nsv467719	chr11:18447611-18542227	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv553634	chr11:18447611-18542227	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18496200-18538000	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr11:18496200-18541200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr11:18496400-18542000	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr11:18496600-18540600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:18496600-18541000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:18500000-18547000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr11:18504000-18540600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:18505200-18531800	Weak transcription	Fetal Brain Male	brain
9	chr11:18509000-18537600	Strong transcription	Liver	Liver
10	chr11:18509000-18540200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:18509000-18540600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr11:18509600-18540200	Strong transcription	Placenta	Placenta
13	chr11:18510800-18541400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr11:18513000-18544000	Weak transcription	Gastric	stomach
15	chr11:18513000-18544000	Weak transcription	Psoas Muscle	Psoas
16	chr11:18513000-18547600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:18513200-18532600	Weak transcription	Esophagus	oesophagus
18	chr11:18514600-18540800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr11:18514800-18539800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr11:18515000-18537600	Strong transcription	Fetal Thymus	thymus
21	chr11:18515000-18540000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:18515000-18540600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:18515200-18538000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:18515400-18547200	Weak transcription	Stomach Mucosa	stomach
25	chr11:18515600-18537600	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr11:18515600-18537800	Strong transcription	Fetal Intestine Large	intestine
27	chr11:18516200-18538200	Strong transcription	Adipose Nuclei	Adipose
28	chr11:18516200-18538800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr11:18516200-18540400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr11:18516400-18531400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr11:18516400-18532200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:18516400-18540400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr11:18516800-18541800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:18517200-18540400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:18517600-18534200	Strong transcription	Primary hematopoietic stem cells	blood
36	chr11:18518000-18539200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr11:18518200-18538600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr11:18518200-18540400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr11:18518400-18530400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr11:18518600-18531800	Weak transcription	Aorta	Aorta
41	chr11:18518600-18537200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr11:18519200-18531400	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr11:18519200-18540600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr11:18519200-18540800	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr11:18519200-18540800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr11:18519400-18540400	Strong transcription	Primary T cells from cord blood	blood
47	chr11:18519800-18529200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr11:18520600-18534800	Weak transcription	Right Ventricle	heart
49	chr11:18521200-18537400	Strong transcription	Primary B cells from cord blood	blood
50	chr11:18521400-18529400	Strong transcription	Brain Germinal Matrix	brain

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