Variant report

Variant	rs12153205
Chromosome Location	chr5:52780586-52780587
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	chr5:52778442..52780466-chr5:52780528..52782611,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134363	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11954686	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152850	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62370509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62370510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62370511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62370518	0.90[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	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52777400-52781800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:52777600-52781200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:52778600-52781800	Transcr. at gene 5' and 3'	NHLF	lung
4	chr5:52778600-52782600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:52778800-52781200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
6	chr5:52778800-52782000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:52779000-52780600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:52779000-52780800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:52779000-52781800	Strong transcription	HSMMtube	muscle
10	chr5:52779000-52782000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:52779000-52782400	Weak transcription	Hela-S3	cervix
12	chr5:52779000-52786000	Weak transcription	Psoas Muscle	Psoas
13	chr5:52779000-52786400	Weak transcription	A549	lung
14	chr5:52779000-52786600	Weak transcription	NH-A	brain
15	chr5:52779200-52783200	Strong transcription	HSMM	muscle
16	chr5:52779200-52784000	Weak transcription	Aorta	Aorta
17	chr5:52779200-52790400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:52779400-52781200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:52779400-52781600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:52779400-52781800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr5:52779400-52782800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:52779400-52783400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:52779400-52786600	Weak transcription	Adipose Nuclei	Adipose
24	chr5:52779400-52786600	Weak transcription	Right Atrium	heart
25	chr5:52779600-52780800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:52779600-52780800	Weak transcription	Placenta	Placenta
27	chr5:52779600-52781200	Strong transcription	Fetal Muscle Trunk	muscle
28	chr5:52779600-52781200	Genic enhancers	NHEK	skin
29	chr5:52779600-52781400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:52779600-52781600	Weak transcription	Fetal Stomach	stomach
31	chr5:52779600-52781800	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr5:52779600-52782000	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:52779600-52782200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:52779600-52782200	Strong transcription	Fetal Muscle Leg	muscle
35	chr5:52779600-52783400	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr5:52779600-52783400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr5:52779600-52784200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr5:52779800-52780800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:52779800-52781200	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:52779800-52783400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr5:52780000-52781200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:52780000-52781200	Genic enhancers	Liver	Liver
43	chr5:52780000-52781200	Genic enhancers	HMEC	breast
44	chr5:52780000-52783400	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr5:52780000-52784000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:52780000-52786600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr5:52780200-52781200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:52780200-52781200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr5:52780200-52781800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr5:52780200-52781800	Genic enhancers	HepG2	liver

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