Variant report

Variant	rs11162333
Chromosome Location	chr1:77865646-77865647
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	chr1:77863743..77865980-chr1:77869588..77871346,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10782648	0.80[JPT][hapmap]
rs11162331	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12132133	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12142918	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12401953	0.91[AMR][1000 genomes]
rs17100308	0.83[JPT][hapmap]
rs17100475	0.88[JPT][hapmap]
rs17100521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs3862894	0.88[JPT][hapmap]
rs3896706	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3911801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6689581	0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs6694630	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7518696	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7520851	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77845200-77878000	Weak transcription	Primary T cells from cord blood	blood
2	chr1:77845200-77878400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:77859800-77866200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:77860000-77866200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:77860000-77866600	Enhancers	Brain Hippocampus Middle	brain
6	chr1:77860800-77866000	Enhancers	Brain Angular Gyrus	brain
7	chr1:77861000-77866400	Enhancers	Brain Substantia Nigra	brain
8	chr1:77861600-77871800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:77862800-77866000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:77863200-77871800	Weak transcription	Aorta	Aorta
11	chr1:77863600-77866000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr1:77864000-77865800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:77864000-77867400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:77864200-77871200	Weak transcription	HSMMtube	muscle
15	chr1:77864400-77870600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:77864600-77866000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:77864800-77865800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:77864800-77866000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:77865000-77865800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:77865000-77865800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:77865000-77866000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:77865000-77867800	Enhancers	NHDF-Ad	bronchial
23	chr1:77865200-77865800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:77865200-77866000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:77865200-77867200	Enhancers	Osteobl	bone
26	chr1:77865600-77866000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:77865600-77866000	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr1:77865600-77866000	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr1:77865600-77866000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr1:77865600-77867000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:77865600-77877200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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