Variant report

Variant	rs4542406
Chromosome Location	chr11:9919291-9919292
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	chr11:9918384..9921801-chr11:9925480..9929741,5	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10500710	0.85[JPT][hapmap]
rs10500711	0.85[JPT][hapmap];0.86[YRI][hapmap]
rs10500713	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10500714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12576435	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1546543	0.85[JPT][hapmap];0.86[YRI][hapmap]
rs16907215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16907238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs16907241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16907248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16907257	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171493	0.85[JPT][hapmap]
rs1996062	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs360162	0.85[JPT][hapmap];0.86[YRI][hapmap]
rs360163	0.85[JPT][hapmap];0.86[YRI][hapmap]
rs360166	0.84[JPT][hapmap]
rs360169	0.85[JPT][hapmap]
rs4463836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs59550065	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60517573	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs938163	0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv2762895	chr11:9849511-9954549	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv896988	chr11:9912052-10012511	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9878800-9952200	Weak transcription	Aorta	Aorta
2	chr11:9882400-9929600	Weak transcription	Primary T cells from cord blood	blood
3	chr11:9892400-9921200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:9894400-9978600	Weak transcription	Left Ventricle	heart
5	chr11:9904000-9937000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:9906800-9920400	Weak transcription	HUVEC	blood vessel
7	chr11:9910000-9954600	Weak transcription	Pancreas	Pancrea
8	chr11:9910200-9921000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr11:9911800-9921200	Weak transcription	HMEC	breast
10	chr11:9913400-9919800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:9913400-9921000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr11:9913600-9921200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr11:9913600-9928800	Weak transcription	Right Ventricle	heart
14	chr11:9913800-9927400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:9914200-9926800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:9914400-9927600	Weak transcription	Brain Anterior Caudate	brain
17	chr11:9915000-9921000	Weak transcription	Hela-S3	cervix
18	chr11:9915000-9937200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:9915200-9922600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:9915400-9921400	Weak transcription	NHLF	lung
21	chr11:9915400-9923200	Weak transcription	HSMMtube	muscle
22	chr11:9915400-9926800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr11:9915400-9927600	Weak transcription	Colon Smooth Muscle	Colon
24	chr11:9915600-9921200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr11:9915600-9923400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr11:9915800-9923000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:9916600-9921400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:9916600-9923000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:9916600-9925200	Weak transcription	Lung	lung
30	chr11:9916600-9932600	Weak transcription	Fetal Intestine Small	intestine
31	chr11:9916800-9921000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr11:9916800-9921800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:9916800-9922800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:9916800-9923600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr11:9916800-9925000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr11:9916800-9944400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr11:9916800-9944400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr11:9917000-9923800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr11:9917000-9927600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr11:9917000-9937200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr11:9917200-9922800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr11:9917200-9923000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr11:9917200-9925000	Weak transcription	Ovary	ovary
44	chr11:9917200-9927400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:9917400-9920200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr11:9917400-9921200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:9917400-9921200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr11:9917400-9921200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr11:9917400-9921800	Weak transcription	Placenta	Placenta
50	chr11:9917400-9928000	Weak transcription	Brain Hippocampus Middle	brain

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