Variant report

Variant	rs12167128
Chromosome Location	chr22:28449353-28449354
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28446750..28449542-chr22:29186576..29188536,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1000112	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10483139	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10483143	0.89[MEX][hapmap]
rs12166077	0.89[MEX][hapmap]
rs12166740	0.89[MEX][hapmap]
rs12169782	0.83[EUR][1000 genomes]
rs12170161	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs130411	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs130414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs135653	0.84[EUR][1000 genomes]
rs138630	0.89[EUR][1000 genomes]
rs138646	0.82[ASW][hapmap]
rs138648	0.82[ASW][hapmap];0.90[MEX][hapmap]
rs138660	0.89[MEX][hapmap]
rs138664	0.89[MEX][hapmap]
rs138676	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs138679	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]
rs138680	0.86[YRI][hapmap]
rs16985967	0.89[MEX][hapmap]
rs17389267	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17480137	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17480369	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17483887	0.89[MEX][hapmap]
rs2038287	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2143420	0.85[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34734418	0.87[EUR][1000 genomes]
rs470101	0.82[ASW][hapmap]
rs470103	0.89[MEX][hapmap]
rs7286795	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7292859	0.88[EUR][1000 genomes]
rs8135697	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs926467	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9620758	0.82[EUR][1000 genomes]
rs9620762	0.89[MEX][hapmap]
rs9620764	0.89[MEX][hapmap]
rs9620768	0.89[MEX][hapmap]
rs9625368	0.83[EUR][1000 genomes]
rs9625378	0.88[EUR][1000 genomes]
rs9625391	0.89[MEX][hapmap]
rs9712839	0.84[AFR][1000 genomes]
rs9985181	0.83[EUR][1000 genomes]

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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12167128	SNORD45A	trans	cerebellum	SCAN
rs12167128	BCR	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28431200-28449600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr22:28431200-28459600	Weak transcription	Aorta	Aorta
3	chr22:28432000-28469000	Weak transcription	Primary T cells from cord blood	blood
4	chr22:28439600-28449800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr22:28439800-28450000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr22:28440000-28450000	Weak transcription	Ovary	ovary
7	chr22:28440200-28449800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr22:28440200-28450000	Weak transcription	NHDF-Ad	bronchial
9	chr22:28440400-28449400	Weak transcription	NHLF	lung
10	chr22:28441000-28452200	Weak transcription	Fetal Intestine Large	intestine
11	chr22:28443800-28459200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr22:28444400-28458800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr22:28444600-28449800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr22:28445200-28462200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr22:28445200-28470400	Weak transcription	Pancreas	Pancrea
16	chr22:28445400-28459200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr22:28445400-28470800	Weak transcription	Lung	lung
18	chr22:28445800-28462800	Weak transcription	Left Ventricle	heart
19	chr22:28446200-28458000	Weak transcription	Fetal Intestine Small	intestine
20	chr22:28446200-28467800	Weak transcription	Fetal Muscle Leg	muscle
21	chr22:28446400-28454000	Weak transcription	Dnd41	blood
22	chr22:28447200-28449800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr22:28447600-28450600	Enhancers	Fetal Brain Male	brain
24	chr22:28447800-28449600	Enhancers	Brain Germinal Matrix	brain
25	chr22:28448000-28449800	Weak transcription	HUVEC	blood vessel
26	chr22:28448200-28449400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr22:28448200-28449600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr22:28448200-28449600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr22:28448400-28449400	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr22:28448400-28449600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr22:28448400-28458000	Weak transcription	Fetal Stomach	stomach
32	chr22:28448600-28449400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr22:28448800-28449400	Flanking Active TSS	Fetal Brain Female	brain
34	chr22:28448800-28450200	Enhancers	Osteobl	bone
35	chr22:28448800-28450800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr22:28449200-28449400	Enhancers	Colon Smooth Muscle	Colon
37	chr22:28449200-28449600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr22:28449200-28449600	Weak transcription	Adipose Nuclei	Adipose
39	chr22:28449200-28449600	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr22:28449200-28454000	Weak transcription	Fetal Lung	lung

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