Variant report

Variant	rs138679
Chromosome Location	chr22:28411748-28411749
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	chr22:28392464..28394711-chr22:28410219..28411871,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235954	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1000112	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10154425	0.89[CEU][hapmap];0.88[MEX][hapmap]
rs10483139	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10483143	1.00[MEX][hapmap]
rs118840	0.89[MEX][hapmap]
rs12166077	0.89[CEU][hapmap];1.00[MEX][hapmap]
rs12166740	1.00[MEX][hapmap]
rs12167128	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[ASN][1000 genomes]
rs12168054	0.89[CEU][hapmap]
rs12168582	0.89[MEX][hapmap]
rs12170161	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12170953	0.89[CEU][hapmap]
rs130411	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs130414	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[ASN][1000 genomes]
rs138630	0.87[ASN][1000 genomes]
rs138636	0.89[MEX][hapmap]
rs138639	0.89[MEX][hapmap]
rs138645	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs138646	1.00[ASW][hapmap];0.81[CEU][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs138648	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs138651	0.86[CEU][hapmap]
rs138652	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs138653	0.89[CEU][hapmap]
rs138654	0.89[CEU][hapmap]
rs138656	0.89[CEU][hapmap]
rs138658	0.89[CEU][hapmap]
rs138660	0.89[CEU][hapmap];1.00[MEX][hapmap]
rs138664	0.89[CEU][hapmap];1.00[MEX][hapmap]
rs138665	0.89[CEU][hapmap]
rs138667	0.89[CEU][hapmap]
rs138671	0.89[CEU][hapmap]
rs138676	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138680	1.00[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16985967	1.00[MEX][hapmap]
rs16986037	0.88[MEX][hapmap]
rs16986077	0.88[MEX][hapmap]
rs17389267	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17407024	0.88[CEU][hapmap]
rs17480137	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17480369	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17483887	0.89[CEU][hapmap];1.00[MEX][hapmap]
rs17484337	0.89[CEU][hapmap]
rs2143420	0.89[MEX][hapmap]
rs2745562	0.86[CEU][hapmap]
rs470101	1.00[ASW][hapmap];0.90[CEU][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs470102	0.89[CEU][hapmap]
rs470103	0.89[CEU][hapmap];1.00[MEX][hapmap]
rs7286795	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7292859	0.87[ASN][1000 genomes]
rs73880371	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8135697	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs926467	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9306452	0.88[MEX][hapmap]
rs9620762	0.89[CEU][hapmap];1.00[MEX][hapmap]
rs9620764	0.89[CEU][hapmap];1.00[MEX][hapmap]
rs9620768	1.00[MEX][hapmap]
rs9620769	0.88[MEX][hapmap]
rs9620770	0.88[MEX][hapmap]
rs9625352	0.89[MEX][hapmap]
rs9625378	0.87[ASN][1000 genomes]
rs9625387	0.89[CEU][hapmap]
rs9625390	0.89[CEU][hapmap]
rs9625391	0.89[CEU][hapmap];1.00[MEX][hapmap]
rs9625408	0.89[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28381800-28412400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr22:28386200-28416000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr22:28389200-28413000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr22:28390000-28414600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr22:28390400-28416200	Weak transcription	Colonic Mucosa	Colon
6	chr22:28394800-28414000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr22:28395000-28416400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr22:28395600-28413000	Weak transcription	Pancreas	Pancrea
9	chr22:28396000-28422400	Weak transcription	Primary T cells from cord blood	blood
10	chr22:28397200-28423000	Weak transcription	HepG2	liver
11	chr22:28397400-28412000	Weak transcription	Placenta	Placenta
12	chr22:28399400-28425800	Weak transcription	Liver	Liver
13	chr22:28401600-28412000	Weak transcription	Thymus	Thymus
14	chr22:28405200-28414000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr22:28405400-28412400	Weak transcription	Brain Hippocampus Middle	brain
16	chr22:28405400-28415000	Weak transcription	HSMM	muscle
17	chr22:28405400-28416200	Weak transcription	NHDF-Ad	bronchial
18	chr22:28405400-28416200	Weak transcription	NHLF	lung
19	chr22:28405400-28416400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr22:28405400-28416400	Weak transcription	Fetal Kidney	kidney
21	chr22:28405600-28412400	Weak transcription	Brain Anterior Caudate	brain
22	chr22:28405600-28414800	Weak transcription	HSMMtube	muscle
23	chr22:28405800-28414000	Weak transcription	Psoas Muscle	Psoas
24	chr22:28405800-28416000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr22:28405800-28416200	Weak transcription	Left Ventricle	heart
26	chr22:28406800-28411800	Weak transcription	Fetal Heart	heart
27	chr22:28407600-28411800	Strong transcription	Dnd41	blood
28	chr22:28408000-28412600	Strong transcription	Stomach Smooth Muscle	stomach
29	chr22:28408600-28411800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr22:28408800-28416200	Genic enhancers	Fetal Muscle Trunk	muscle
31	chr22:28409000-28428000	Genic enhancers	Fetal Muscle Leg	muscle
32	chr22:28409200-28412600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr22:28409200-28416200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr22:28409400-28412400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr22:28409400-28415800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr22:28409400-28430400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr22:28409600-28416000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr22:28409800-28412800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr22:28410000-28412000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr22:28410000-28413200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr22:28410000-28414400	Enhancers	Fetal Brain Male	brain
42	chr22:28410000-28415000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr22:28410000-28416000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr22:28410200-28411800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr22:28410200-28415200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr22:28410200-28415800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr22:28410200-28416000	Weak transcription	Brain Substantia Nigra	brain
48	chr22:28410200-28423000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr22:28410200-28423400	Weak transcription	Gastric	stomach
50	chr22:28410400-28412200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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