Variant report

Variant	rs1546327
Chromosome Location	chr11:19139622-19139623
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	chr11:19081397..19083267-chr11:19138143..19140482,2	MCF-7	breast:
2	chr11:19138213..19140336-chr11:19296347..19298663,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254544	Chromatin interaction
ENSG00000183695	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10500841	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs10741761	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs10766528	0.92[EUR][1000 genomes]
rs10833064	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs10833065	0.92[EUR][1000 genomes]
rs11025025	0.93[EUR][1000 genomes]
rs11025026	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs11025028	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11025037	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs11604471	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11604483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11606057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11607797	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs12270581	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs12273085	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12801321	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1393957	0.81[JPT][hapmap]
rs1503506	0.94[CEU][hapmap];0.80[YRI][hapmap];0.92[EUR][1000 genomes]
rs1503507	0.94[CEU][hapmap];0.81[YRI][hapmap];0.92[EUR][1000 genomes]
rs1503508	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2042687	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2042688	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs2134622	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs2271001	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs28891775	0.87[EUR][1000 genomes]
rs3802796	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs3802797	0.89[EUR][1000 genomes]
rs3802798	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4515942	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4756990	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4757757	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs4757758	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs4757759	0.89[EUR][1000 genomes]
rs4757760	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs7111105	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs7129212	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs7129326	0.92[EUR][1000 genomes]
rs7950603	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs7950788	0.92[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	nsv1040805	chr11:19037871-19892803	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv540957	chr11:19037871-19892803	Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:19138000-19139800	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr11:19138000-19139800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr11:19138000-19140000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:19138000-19140200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr11:19138200-19139800	Active TSS	H9 Cell Line	embryonic stem cell
6	chr11:19138200-19139800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:19138200-19139800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:19138200-19139800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
9	chr11:19138200-19139800	Active TSS	NHLF	lung
10	chr11:19138200-19140000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:19138200-19140000	Flanking Active TSS	Brain Germinal Matrix	brain
12	chr11:19138200-19140000	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr11:19138200-19140000	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr11:19138200-19140000	Active TSS	NHDF-Ad	bronchial
15	chr11:19138400-19139800	Active TSS	H1 Cell Line	embryonic stem cell
16	chr11:19138400-19139800	Active TSS	Fetal Intestine Large	intestine
17	chr11:19138400-19140000	Active TSS	Brain Anterior Caudate	brain
18	chr11:19138600-19139800	Active TSS	Brain Hippocampus Middle	brain
19	chr11:19139000-19140000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr11:19139000-19140000	Flanking Active TSS	Fetal Brain Male	brain
21	chr11:19139200-19139800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:19139200-19139800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:19139200-19139800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr11:19139200-19139800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr11:19139200-19139800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr11:19139200-19139800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr11:19139200-19139800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:19139200-19139800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:19139200-19139800	Flanking Active TSS	Rectal Smooth Muscle	rectum
30	chr11:19139200-19139800	Flanking Active TSS	K562	blood
31	chr11:19139200-19140000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:19139200-19140000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr11:19139200-19140000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr11:19139200-19140000	Flanking Active TSS	NH-A	brain
35	chr11:19139200-19140200	Flanking Active TSS	Dnd41	blood
36	chr11:19139200-19141200	Flanking Active TSS	HUVEC	blood vessel
37	chr11:19139400-19139800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:19139400-19139800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr11:19139400-19139800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
40	chr11:19139400-19139800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr11:19139400-19139800	Enhancers	Liver	Liver
42	chr11:19139400-19139800	Flanking Active TSS	Fetal Intestine Small	intestine
43	chr11:19139400-19139800	Flanking Active TSS	Fetal Kidney	kidney
44	chr11:19139400-19139800	Flanking Active TSS	Fetal Lung	lung
45	chr11:19139400-19139800	Flanking Active TSS	Stomach Mucosa	stomach
46	chr11:19139400-19139800	Flanking Active TSS	HMEC	breast
47	chr11:19139400-19140000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr11:19139400-19140000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr11:19139400-19140000	Flanking Active TSS	A549	lung
50	chr11:19139400-19140200	Enhancers	Primary monocytes fromperipheralblood	blood

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