Variant report

Variant	rs12477510
Chromosome Location	chr2:134332656-134332657
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	chr1:115534913..115537064-chr2:134331546..134333368,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11693982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12691837	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12691838	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13002374	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1347043	0.95[CHB][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1816382	0.81[CEU][hapmap];0.94[CHB][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4954067	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56296323	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs891821	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs978098	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
4	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv516644	chr2:134301130-134391214	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv431713	chr2:134316522-134413604	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1013713	chr2:134322236-134644574	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv535931	chr2:134322236-134644574	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134325000-134342400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:134326200-134337000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:134326400-134334200	Weak transcription	Liver	Liver
4	chr2:134326400-134336200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:134326400-134337000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:134326600-134334000	Weak transcription	NHEK	skin
7	chr2:134326600-134334200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:134326600-134334600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:134326600-134336000	Weak transcription	Brain Anterior Caudate	brain
10	chr2:134326600-134344200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:134329200-134334600	Weak transcription	Fetal Intestine Large	intestine
12	chr2:134330200-134333200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:134330200-134339800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:134331000-134334200	Enhancers	Fetal Heart	heart
15	chr2:134331800-134332800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:134331800-134332800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:134331800-134332800	Enhancers	HUVEC	blood vessel
18	chr2:134332000-134332800	Enhancers	Fetal Muscle Leg	muscle
19	chr2:134332000-134332800	Enhancers	NH-A	brain
20	chr2:134332000-134339000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:134332200-134339800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:134332400-134332800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:134332400-134332800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:134332400-134332800	Enhancers	Brain Hippocampus Middle	brain
25	chr2:134332400-134332800	Enhancers	HMEC	breast
26	chr2:134332400-134333800	Enhancers	Pancreas	Pancrea
27	chr2:134332400-134334000	Enhancers	Esophagus	oesophagus
28	chr2:134332600-134333200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:134332600-134333400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:134332600-134334200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:134332600-134334400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:134332600-134334600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:134332600-134335800	Weak transcription	Brain Substantia Nigra	brain
34	chr2:134332600-134338800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr2:134332600-134338800	Weak transcription	Right Atrium	heart

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