Variant report

Variant	rs12290460
Chromosome Location	chr11:56959783-56959784
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:56946370..56948285-chr11:56958607..56960284,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11228901	1.00[AMR][1000 genomes]
rs11501564	1.00[AMR][1000 genomes]
rs12275563	1.00[AMR][1000 genomes]
rs12275655	1.00[AMR][1000 genomes]
rs12277644	1.00[AMR][1000 genomes]
rs12288446	1.00[AMR][1000 genomes]
rs12289270	1.00[AMR][1000 genomes]
rs12290493	1.00[AMR][1000 genomes]
rs2860248	1.00[AMR][1000 genomes]
rs2860249	1.00[AMR][1000 genomes]
rs2860311	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2860313	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2860510	1.00[AMR][1000 genomes]
rs2957193	1.00[AMR][1000 genomes]
rs2960567	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3016754	1.00[AMR][1000 genomes]
rs3017570	1.00[AMR][1000 genomes]
rs3018193	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7111423	1.00[MEX][hapmap]
rs73474661	1.00[AMR][1000 genomes]
rs73474667	1.00[AMR][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	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv482317	chr11:56857026-57028631	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12290460	CCDC19	trans	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:56949400-56962600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:56950200-56960400	Weak transcription	Right Ventricle	heart
3	chr11:56950200-56969800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:56952600-56967000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr11:56955800-56962600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:56958400-56959800	Enhancers	Fetal Brain Male	brain
7	chr11:56958400-56960000	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr11:56958400-56960000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr11:56958400-56960400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr11:56958600-56959800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:56958600-56959800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr11:56958600-56960000	Enhancers	Adipose Nuclei	Adipose
13	chr11:56958800-56959800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr11:56958800-56960000	Enhancers	Fetal Brain Female	brain
15	chr11:56959200-56960000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr11:56959200-56960000	Enhancers	Psoas Muscle	Psoas
17	chr11:56959400-56959800	Enhancers	Right Atrium	heart
18	chr11:56959400-56960000	Enhancers	Spleen	Spleen
19	chr11:56959600-56959800	Enhancers	Fetal Muscle Leg	muscle
20	chr11:56959600-56960000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr11:56959600-56960000	Enhancers	Brain Germinal Matrix	brain
22	chr11:56959600-56960400	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr11:56959600-56964000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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