Variant report

Variant	rs2649908
Chromosome Location	chr12:123306547-123306548
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123305427..123307833-chr12:123319941..123322774,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130787	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10773627	0.89[ASN][1000 genomes]
rs10773657	0.89[ASN][1000 genomes]
rs10847826	0.89[ASN][1000 genomes]
rs10847869	0.89[ASN][1000 genomes]
rs11060064	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11060065	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11060208	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11060209	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12297553	0.90[EUR][1000 genomes]
rs12298151	0.86[ASN][1000 genomes]
rs12298293	0.86[EUR][1000 genomes]
rs12298664	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12299742	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12313006	0.83[ASN][1000 genomes]
rs12313538	0.86[EUR][1000 genomes]
rs12313600	0.86[EUR][1000 genomes]
rs12314494	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12314544	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12315520	0.86[EUR][1000 genomes]
rs12319654	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12321131	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12426809	0.89[ASN][1000 genomes]
rs1532835	0.87[ASN][1000 genomes]
rs1671685	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1696326	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1696349	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1799618	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1979236	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1979237	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2100500	0.99[ASN][1000 genomes]
rs2135014	0.87[ASN][1000 genomes]
rs2271051	0.84[ASN][1000 genomes]
rs2292131	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292132	0.87[ASN][1000 genomes]
rs2292134	0.85[ASN][1000 genomes]
rs2292135	0.84[ASN][1000 genomes]
rs2292136	0.81[ASN][1000 genomes]
rs2292139	0.82[ASN][1000 genomes]
rs2343108	0.87[ASN][1000 genomes]
rs2343685	0.89[ASN][1000 genomes]
rs2649909	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2880678	0.89[ASN][1000 genomes]
rs3817094	0.86[ASN][1000 genomes]
rs3852536	0.85[ASN][1000 genomes]
rs4759355	0.94[ASN][1000 genomes]
rs4759389	0.89[ASN][1000 genomes]
rs4759392	0.82[ASN][1000 genomes]
rs56272219	0.99[ASN][1000 genomes]
rs58182048	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59192320	0.84[ASN][1000 genomes]
rs59922385	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60308342	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7294991	0.82[ASN][1000 genomes]
rs7303024	0.99[ASN][1000 genomes]
rs7309225	0.82[ASN][1000 genomes]
rs73421642	0.99[ASN][1000 genomes]
rs735378	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7398546	0.83[ASN][1000 genomes]
rs754080	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs839360	0.86[EUR][1000 genomes]
rs897391	0.89[ASN][1000 genomes]
rs897392	0.89[ASN][1000 genomes]
rs897393	0.89[ASN][1000 genomes]
rs921808	0.87[ASN][1000 genomes]
rs936083	0.81[ASN][1000 genomes]
rs937520	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs937766	0.87[ASN][1000 genomes]
rs9788290	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123259400-123310600	Weak transcription	HSMMtube	muscle
2	chr12:123259800-123310600	Weak transcription	Brain Substantia Nigra	brain
3	chr12:123290600-123310400	Weak transcription	Aorta	Aorta
4	chr12:123296400-123310200	Weak transcription	Fetal Intestine Small	intestine
5	chr12:123298000-123310600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:123298400-123310400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:123299600-123310600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:123302200-123312000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:123302600-123310200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:123304000-123308800	Weak transcription	Gastric	stomach
11	chr12:123304200-123310600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:123304200-123310600	Weak transcription	Fetal Brain Female	brain
13	chr12:123304400-123310400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:123304400-123312000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:123305800-123309000	Enhancers	Primary B cells from peripheral blood	blood
16	chr12:123305800-123310400	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:123305800-123310600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:123305800-123318800	Weak transcription	Pancreas	Pancrea
19	chr12:123306000-123307200	Weak transcription	K562	blood
20	chr12:123306000-123308600	Enhancers	Primary B cells from cord blood	blood
21	chr12:123306200-123310600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr12:123306400-123307200	Enhancers	Fetal Brain Male	brain

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