Variant report

Variant	rs2554861
Chromosome Location	chr12:51341331-51341332
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51336604..51339299-chr12:51340457..51342342,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs150909	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs161044	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs161045	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs161046	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs161047	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2046498	0.92[EUR][1000 genomes]
rs224564	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs224566	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs224569	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs224570	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs224573	0.83[AMR][1000 genomes]
rs224574	0.83[AMR][1000 genomes]
rs224578	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs224585	0.80[EUR][1000 genomes]
rs224586	0.83[AMR][1000 genomes]
rs224590	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs224592	0.82[EUR][1000 genomes]
rs224593	0.82[EUR][1000 genomes]
rs2554858	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554859	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630353	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630358	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2630362	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2630366	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630367	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs319930	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319938	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319940	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319941	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319943	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390424	0.82[EUR][1000 genomes]
rs445520	0.82[EUR][1000 genomes]
rs452587	0.83[AMR][1000 genomes]
rs4768875	0.83[AMR][1000 genomes]
rs55874852	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706803	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs706804	0.88[EUR][1000 genomes]
rs7138860	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829016	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829021	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs853236	0.83[AMR][1000 genomes];0.92[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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2554861	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51319400-51346200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51323000-51377200	Weak transcription	Aorta	Aorta
3	chr12:51328800-51378000	Weak transcription	Brain Substantia Nigra	brain
4	chr12:51329200-51341600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr12:51329600-51373600	Weak transcription	Left Ventricle	heart
6	chr12:51331400-51378400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:51331600-51373800	Weak transcription	Pancreas	Pancrea
8	chr12:51331800-51342800	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:51331800-51343000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr12:51331800-51353800	Weak transcription	Primary T cells from cord blood	blood
11	chr12:51331800-51382000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:51331800-51382000	Weak transcription	Ovary	ovary
13	chr12:51332000-51346400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:51332400-51343600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:51332400-51346200	Weak transcription	Fetal Intestine Small	intestine
16	chr12:51332400-51346200	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:51332400-51346200	Weak transcription	Fetal Stomach	stomach
18	chr12:51332600-51346400	Weak transcription	Brain Angular Gyrus	brain
19	chr12:51332600-51354400	Weak transcription	Thymus	Thymus
20	chr12:51332600-51365000	Weak transcription	Fetal Brain Female	brain
21	chr12:51340000-51361800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:51340800-51342400	Enhancers	HSMMtube	muscle
23	chr12:51341200-51341400	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr12:51341200-51341800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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