Variant report

Variant	rs12229297
Chromosome Location	chr12:103965032-103965033
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	chr12:103964010..103966292-chr12:103967162..103970095,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10507167	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1070073	0.82[ASN][1000 genomes]
rs10861037	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10861038	0.89[ASN][1000 genomes]
rs1104981	1.00[ASN][1000 genomes]
rs11111649	0.88[ASN][1000 genomes]
rs11111659	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111661	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111662	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111663	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111667	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111668	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11111670	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11532373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11831074	0.88[ASN][1000 genomes]
rs11835633	0.88[ASN][1000 genomes]
rs12578790	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12579074	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17034112	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17034125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17034140	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2723889	0.82[ASN][1000 genomes]
rs4321042	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12229297	STAB2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:103961000-103968800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:103964600-103966000	Enhancers	Placenta Amnion	Placenta Amnion
3	chr12:103964800-103965200	Flanking Active TSS	HSMMtube	muscle
4	chr12:103964800-103965400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:103964800-103965400	Active TSS	Brain Anterior Caudate	brain
6	chr12:103964800-103965600	Active TSS	Brain Substantia Nigra	brain
7	chr12:103965000-103965200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
8	chr12:103965000-103965200	Flanking Active TSS	H9 Cell Line	embryonic stem cell
9	chr12:103965000-103965200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
10	chr12:103965000-103965200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr12:103965000-103965200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr12:103965000-103965200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:103965000-103965200	Active TSS	Brain Cingulate Gyrus	brain
14	chr12:103965000-103965200	Flanking Active TSS	Brain Germinal Matrix	brain
15	chr12:103965000-103965200	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr12:103965000-103965200	Enhancers	Esophagus	oesophagus
17	chr12:103965000-103965200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr12:103965000-103965200	Active TSS	Left Ventricle	heart
19	chr12:103965000-103965200	Active TSS	Right Ventricle	heart
20	chr12:103965000-103965200	Enhancers	NH-A	brain
21	chr12:103965000-103965400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:103965000-103965400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:103965000-103965400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr12:103965000-103965400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
25	chr12:103965000-103965400	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr12:103965000-103965400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:103965000-103965400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:103965000-103965400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:103965000-103965400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:103965000-103965400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:103965000-103965400	Enhancers	Fetal Brain Male	brain
32	chr12:103965000-103965400	Active TSS	Fetal Brain Female	brain
33	chr12:103965000-103965400	Active TSS	Fetal Intestine Large	intestine
34	chr12:103965000-103965400	Flanking Active TSS	Fetal Intestine Small	intestine
35	chr12:103965000-103965400	Enhancers	Fetal Muscle Leg	muscle
36	chr12:103965000-103965400	Enhancers	Gastric	stomach
37	chr12:103965000-103965400	Enhancers	Psoas Muscle	Psoas
38	chr12:103965000-103965400	Active TSS	Rectal Smooth Muscle	rectum
39	chr12:103965000-103965400	Flanking Active TSS	HSMM	muscle
40	chr12:103965000-103965400	Flanking Active TSS	NHEK	skin
41	chr12:103965000-103965600	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr12:103965000-103965600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:103965000-103965600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:103965000-103965600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:103965000-103965600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:103965000-103965600	Active TSS	Stomach Smooth Muscle	stomach
47	chr12:103965000-103965600	Enhancers	HMEC	breast
48	chr12:103965000-103965800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr12:103965000-103966000	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr12:103965000-103966400	Enhancers	Fetal Heart	heart

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