Variant report

Variant	rs1796162
Chromosome Location	chr12:83336849-83336850
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	chr12:83331086..83333520-chr12:83336090..83338497,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10746262	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10778918	1.00[CEU][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10778921	0.94[EUR][1000 genomes]
rs1655611	0.94[EUR][1000 genomes]
rs1655612	0.94[EUR][1000 genomes]
rs1682567	0.90[EUR][1000 genomes]
rs1682575	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs1682579	0.90[EUR][1000 genomes]
rs1682580	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs1682606	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1682607	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1682608	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1796150	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1796156	0.89[CEU][hapmap]
rs1796157	0.94[EUR][1000 genomes]
rs1796161	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1796166	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1796167	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1796168	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1796178	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs1796187	0.96[EUR][1000 genomes]
rs1796296	0.94[EUR][1000 genomes]
rs1796300	0.90[EUR][1000 genomes]
rs1821444	0.94[EUR][1000 genomes]
rs1972801	0.94[EUR][1000 genomes]
rs2046417	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs2062357	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2403025	0.94[EUR][1000 genomes]
rs2403026	0.94[EUR][1000 genomes]
rs2707753	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2707754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2707760	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs2708000	0.92[EUR][1000 genomes]
rs2708001	0.89[CEU][hapmap]
rs4882531	0.94[EUR][1000 genomes]
rs6539697	0.88[EUR][1000 genomes]
rs7297707	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs7299175	0.94[EUR][1000 genomes]
rs7303058	0.94[EUR][1000 genomes]
rs7953974	1.00[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv469490	chr12:83089431-83507269	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv559542	chr12:83089431-83507269	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	esv2758315	chr12:83101045-83357621	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv2759911	chr12:83101045-83357621	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv832472	chr12:83248283-83419753	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
7	nsv559557	chr12:83334204-83453620	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83325000-83346400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:83325600-83348000	Weak transcription	Colon Smooth Muscle	Colon
3	chr12:83326000-83340200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:83331400-83348000	Weak transcription	Brain Hippocampus Middle	brain
5	chr12:83335200-83340200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr12:83336200-83337200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:83336400-83337000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr12:83336400-83337200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:83336400-83337200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:83336400-83337200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr12:83336400-83338600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:83336600-83337000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:83336600-83337200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr12:83336800-83337200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:83336800-83337200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr12:83336800-83337200	Enhancers	Brain Anterior Caudate	brain
17	chr12:83336800-83337200	Enhancers	Brain Substantia Nigra	brain
18	chr12:83336800-83337200	Enhancers	Fetal Lung	lung
19	chr12:83336800-83337200	Enhancers	Fetal Stomach	stomach
20	chr12:83336800-83337400	Enhancers	Rectal Smooth Muscle	rectum
21	chr12:83336800-83337800	Enhancers	Fetal Heart	heart

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