Variant report

Variant	rs12228658
Chromosome Location	chr12:44277314-44277315
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	chr12:44228150..44229800-chr12:44275974..44278416,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139173	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11182298	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11182299	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11182300	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11182301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11182303	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11182304	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11182305	0.97[ASN][1000 genomes]
rs11182308	1.00[ASN][1000 genomes]
rs11182310	1.00[ASN][1000 genomes]
rs11182314	0.97[ASN][1000 genomes]
rs11182323	0.94[ASN][1000 genomes]
rs11182331	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs11182334	0.81[ASN][1000 genomes]
rs11182336	0.81[ASN][1000 genomes]
rs12227646	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12229491	1.00[ASN][1000 genomes]
rs12229940	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12230284	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12230727	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12230751	1.00[ASN][1000 genomes]
rs12231136	0.91[ASN][1000 genomes]
rs12231953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1675761	1.00[CEU][hapmap]
rs1675763	1.00[CEU][hapmap]
rs17093804	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1731426	1.00[CEU][hapmap]
rs1731432	1.00[JPT][hapmap]
rs1948516	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3829807	1.00[ASN][1000 genomes]
rs4488262	1.00[CEU][hapmap]
rs61930682	1.00[ASN][1000 genomes]
rs7136340	1.00[CEU][hapmap];0.81[MKK][hapmap]
rs720944	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7294490	1.00[CEU][hapmap]
rs7296222	1.00[ASN][1000 genomes]
rs73096926	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs73096957	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73096960	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73096982	0.86[EUR][1000 genomes]
rs73098813	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73098867	0.90[AFR][1000 genomes]
rs73098870	0.90[AFR][1000 genomes]
rs766961	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs766962	1.00[CEU][hapmap];0.83[MKK][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933142	chr12:44130156-44278300	Active TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899048	chr12:44209423-44307888	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44240400-44293000	Weak transcription	Aorta	Aorta
2	chr12:44256400-44285600	Weak transcription	HSMMtube	muscle
3	chr12:44263800-44277600	Weak transcription	Left Ventricle	heart
4	chr12:44273800-44278400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:44274600-44278600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:44274600-44286000	Weak transcription	Pancreas	Pancrea
7	chr12:44275000-44278400	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:44275000-44281200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr12:44275200-44277800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:44276600-44278600	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr12:44276800-44278400	Weak transcription	Brain Anterior Caudate	brain
12	chr12:44276800-44278600	Enhancers	Osteobl	bone
13	chr12:44277000-44277400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:44277000-44278600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:44277000-44279600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:44277200-44277600	Enhancers	HSMM	muscle
17	chr12:44277200-44278600	Enhancers	HMEC	breast

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