Variant report

Variant	rs2405516
Chromosome Location	chr1:224858482-224858483
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	chr1:224850263..224854124-chr1:224858225..224860779,3	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10429870	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10915687	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10915698	0.80[CHB][hapmap];0.81[ASN][1000 genomes]
rs12025142	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1369847	0.86[CHB][hapmap];0.88[ASN][1000 genomes]
rs1436169	0.85[ASN][1000 genomes]
rs1436172	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs169888	0.82[JPT][hapmap]
rs2050626	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2050627	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs298735	0.92[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs298739	0.97[ASN][1000 genomes]
rs2993124	0.97[ASN][1000 genomes]
rs3012185	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4653402	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4653404	0.85[ASN][1000 genomes]
rs4653591	0.88[ASN][1000 genomes]
rs4653592	0.85[CHB][hapmap];0.88[ASN][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	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224832200-224884400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:224832800-224869000	Weak transcription	Dnd41	blood
3	chr1:224833200-224874400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:224851400-224863000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:224856200-224858600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:224856200-224858600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:224856200-224858600	Enhancers	NHDF-Ad	bronchial
8	chr1:224856600-224858600	Enhancers	Fetal Muscle Leg	muscle
9	chr1:224857000-224862600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:224857200-224860800	Weak transcription	Left Ventricle	heart
11	chr1:224857200-224860800	Weak transcription	Ovary	ovary
12	chr1:224857200-224869000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:224857200-224869200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:224857400-224860200	Weak transcription	Fetal Brain Male	brain
15	chr1:224857400-224860600	Weak transcription	Fetal Heart	heart
16	chr1:224857400-224860600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:224857400-224860800	Weak transcription	Fetal Stomach	stomach
18	chr1:224857400-224860800	Weak transcription	Pancreas	Pancrea
19	chr1:224857400-224861000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:224858400-224871800	Weak transcription	NHLF	lung
21	chr1:224858400-224874200	Weak transcription	NH-A	brain

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