Variant report

Variant	rs10506089
Chromosome Location	chr12:32660441-32660442
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	chr12:32550963..32552708-chr12:32659377..32661100,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139132	Chromatin interaction

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

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

rs_ID	r²[population]
rs10506088	0.89[ASW][hapmap];0.90[LWK][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs10506091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11052047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16919974	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs57830844	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7308649	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73301589	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74072401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74072613	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9943832	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv898970	chr12:32622097-32680236	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32649000-32660800	Weak transcription	Thymus	Thymus
2	chr12:32655200-32661600	Weak transcription	Spleen	Spleen
3	chr12:32655200-32686000	Weak transcription	Lung	lung
4	chr12:32655400-32661000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:32656000-32661000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:32656000-32666000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:32656000-32668000	Weak transcription	Fetal Thymus	thymus
8	chr12:32656200-32662600	Weak transcription	HepG2	liver
9	chr12:32656200-32668000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:32656400-32685800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:32657000-32661000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr12:32657000-32661800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr12:32657200-32662200	Enhancers	Fetal Heart	heart
14	chr12:32657400-32661400	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr12:32658400-32660800	Weak transcription	Brain Angular Gyrus	brain
16	chr12:32658400-32660800	Weak transcription	Right Ventricle	heart
17	chr12:32658400-32661000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr12:32658600-32660800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:32658600-32667800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:32658600-32682000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr12:32658800-32660800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:32659200-32660800	Weak transcription	Brain Substantia Nigra	brain
23	chr12:32659200-32664400	Weak transcription	NHEK	skin
24	chr12:32659400-32660600	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr12:32659400-32660800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr12:32659400-32665800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:32659400-32667000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:32659600-32660600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr12:32659600-32660600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:32659600-32660600	Weak transcription	Liver	Liver
31	chr12:32659600-32660600	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:32659600-32660800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:32659600-32660800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:32659600-32660800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr12:32659600-32660800	Weak transcription	Fetal Brain Female	brain
36	chr12:32659600-32660800	Weak transcription	Left Ventricle	heart
37	chr12:32659600-32660800	Weak transcription	Ovary	ovary
38	chr12:32659600-32660800	Weak transcription	Psoas Muscle	Psoas
39	chr12:32659600-32660800	Weak transcription	Right Atrium	heart
40	chr12:32659600-32661000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:32659600-32661000	Weak transcription	Brain Germinal Matrix	brain
42	chr12:32659600-32661000	Weak transcription	Esophagus	oesophagus
43	chr12:32659600-32661000	Weak transcription	Pancreas	Pancrea
44	chr12:32659600-32661200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:32659600-32661400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:32659600-32662600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:32659600-32662600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:32659600-32663400	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr12:32659600-32668000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr12:32659600-32675200	Weak transcription	Fetal Stomach	stomach

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