Variant report

Variant	rs12739936
Chromosome Location	chr1:222183189-222183190
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:222182915..222183415-chr17:56708466..56709159,2	MCF-7	breast:
2	chr1:221914275..221916996-chr1:222181914..222184462,2	MCF-7	breast:
3	chr1:221651148..221651987-chr1:222182537..222183210,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143507	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11118926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024555	0.81[EUR][1000 genomes]
rs12025565	0.84[EUR][1000 genomes]
rs12029332	0.86[EUR][1000 genomes]
rs12032653	0.86[EUR][1000 genomes]
rs12032715	0.80[EUR][1000 genomes]
rs12033415	0.92[EUR][1000 genomes]
rs12121134	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125368	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125383	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12129860	0.86[EUR][1000 genomes]
rs12135286	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12140604	0.92[EUR][1000 genomes]
rs12731064	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011182	0.92[EUR][1000 genomes]
rs17011200	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17442058	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442323	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17495159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35212520	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35718308	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35805428	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56170536	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66732677	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687758	0.92[EUR][1000 genomes]
rs6691195	0.92[EUR][1000 genomes]
rs6695584	0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014333	chr1:222131785-222245578	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12739936	RP11-400N13.2	cis	lung	GTEx
rs12739936	RP11-815M8.1	cis	lung	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222169200-222184000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:222181000-222183200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:222182400-222183200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr1:222182400-222183200	Enhancers	NHDF-Ad	bronchial
5	chr1:222182400-222184000	Enhancers	Osteobl	bone
6	chr1:222182600-222183200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr1:222182600-222183200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:222182600-222183400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:222182800-222183200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr1:222182800-222183200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:222182800-222183400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:222182800-222183800	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr1:222183000-222183200	Enhancers	Muscle Satellite Cultured Cells	--

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