Variant report

Variant	rs13407949
Chromosome Location	chr2:134181178-134181179
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:134179232..134182620-chr2:134183188..134186859,3	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10171952	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13386261	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13392676	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13396831	0.82[TSI][hapmap]
rs13401022	0.84[AMR][1000 genomes]
rs13417230	0.80[MEX][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1369510	0.85[TSI][hapmap]
rs58227168	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73957086	0.88[AMR][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	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1002488	chr2:133890159-134275312	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv535928	chr2:133890159-134275312	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv3375790	chr2:133906915-134222833	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv834384	chr2:134005229-134188648	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134171400-134183800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:134174200-134182800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:134175200-134182800	Weak transcription	NHDF-Ad	bronchial
4	chr2:134177800-134181400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:134178200-134181200	Enhancers	NHEK	skin
6	chr2:134178200-134185200	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr2:134178400-134183200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:134178600-134183600	Enhancers	Brain Substantia Nigra	brain
9	chr2:134178800-134183600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr2:134179000-134181200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:134179000-134181200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:134179000-134181400	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr2:134179000-134183200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:134179200-134181200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:134179200-134181400	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr2:134179600-134181600	Enhancers	Fetal Lung	lung
17	chr2:134179800-134181400	Enhancers	A549	lung
18	chr2:134179800-134182200	Weak transcription	NH-A	brain
19	chr2:134180000-134182000	Weak transcription	Pancreas	Pancrea
20	chr2:134180600-134181200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr2:134180800-134182200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:134180800-134182400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:134180800-134182600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:134181000-134181400	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr2:134181000-134181400	Enhancers	Hela-S3	cervix
26	chr2:134181000-134182200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:134181000-134182200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:134181000-134182200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:134181000-134182400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:134181000-134182400	Weak transcription	Brain Anterior Caudate	brain
31	chr2:134181000-134182600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:134181000-134182600	Weak transcription	Brain Germinal Matrix	brain
33	chr2:134181000-134182600	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:134181000-134182800	Weak transcription	Fetal Kidney	kidney
35	chr2:134181000-134183200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:134181000-134183600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr2:134181000-134186800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:134181000-134188200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:134181000-134188200	Weak transcription	HMEC	breast
40	chr2:134181000-134188800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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