Variant report

Variant	rs2540246
Chromosome Location	chr2:39914217-39914218
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39605627..39608331-chr2:39913842..39916545,2	MCF-7	breast:
2	chr2:39892126..39893680-chr2:39911283..39914274,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152154	Chromatin interaction
ENSG00000011566	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs17024242	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2540230	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2540231	1.00[AMR][1000 genomes]
rs2540232	1.00[AMR][1000 genomes]
rs2540237	1.00[AMR][1000 genomes]
rs2540238	0.85[AFR][1000 genomes]
rs2540239	0.85[AFR][1000 genomes]
rs2540240	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716680	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716689	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716695	0.80[YRI][hapmap];1.00[AMR][1000 genomes]
rs2716696	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716708	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716710	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716723	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716725	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2716728	1.00[AMR][1000 genomes]
rs2716731	0.93[LWK][hapmap];0.88[MKK][hapmap];1.00[AMR][1000 genomes]
rs57481251	1.00[AMR][1000 genomes]
rs6746083	1.00[AMR][1000 genomes]
rs73924911	1.00[AMR][1000 genomes]
rs73924912	1.00[AMR][1000 genomes]
rs73924913	1.00[AMR][1000 genomes]
rs73924914	1.00[AMR][1000 genomes]
rs73924935	1.00[AMR][1000 genomes]
rs73924936	1.00[AMR][1000 genomes]
rs7559933	1.00[AMR][1000 genomes]
rs917968	1.00[AMR][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	nsv873889	chr2:39830183-39950482	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39905400-39916600	Enhancers	Fetal Heart	heart
2	chr2:39907600-39922200	Weak transcription	HSMM	muscle
3	chr2:39911800-39915000	Enhancers	Right Atrium	heart
4	chr2:39911800-39915800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:39911800-39916200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr2:39912400-39914400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:39913000-39914800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:39913200-39914400	Enhancers	Fetal Brain Male	brain
9	chr2:39913200-39915600	Weak transcription	Left Ventricle	heart
10	chr2:39913400-39914400	Weak transcription	Lung	lung
11	chr2:39913400-39915400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:39913400-39917200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:39913600-39914800	Weak transcription	Brain Germinal Matrix	brain
14	chr2:39913600-39914800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr2:39913800-39914800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:39913800-39916600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:39914000-39915600	Weak transcription	Fetal Brain Female	brain
18	chr2:39914000-39916400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:39914000-39918800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:39914200-39914400	Enhancers	Brain Anterior Caudate	brain
21	chr2:39914200-39917000	Weak transcription	Aorta	Aorta
22	chr2:39914200-39926800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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