Variant report

Variant	rs12413399
Chromosome Location	chr10:21646236-21646237
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:21645217..21648028-chr10:21658321..21660402,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11012680	0.86[EUR][1000 genomes]
rs11594245	0.89[GIH][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs11595231	0.97[EUR][1000 genomes]
rs11597239	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11597707	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16921724	0.81[EUR][1000 genomes]
rs16921771	1.00[GIH][hapmap]
rs16921796	0.84[EUR][1000 genomes]
rs2039029	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34297119	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35841043	1.00[EUR][1000 genomes]
rs55773472	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55953944	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59781699	0.84[EUR][1000 genomes]
rs6415965	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7069583	0.89[GIH][hapmap];0.81[TSI][hapmap]
rs7071130	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7079617	0.94[EUR][1000 genomes]
rs7080007	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081480	1.00[GIH][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs7089695	1.00[EUR][1000 genomes]
rs7098870	0.94[EUR][1000 genomes]
rs72793050	0.80[EUR][1000 genomes]
rs72793061	0.94[EUR][1000 genomes]
rs72793067	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72793075	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72793077	0.91[EUR][1000 genomes]
rs72793079	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72793086	0.87[EUR][1000 genomes]
rs72793090	0.84[EUR][1000 genomes]
rs7893639	0.94[EUR][1000 genomes];1.00[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	nsv530148	chr10:21065080-21724565	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv831807	chr10:21509185-21688043	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:21639600-21650800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:21639600-21650800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr10:21639600-21652000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:21640800-21648000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr10:21641600-21650000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr10:21644800-21646400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr10:21645200-21648000	Weak transcription	A549	lung
8	chr10:21645200-21650800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr10:21645200-21651000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr10:21645200-21651000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr10:21645400-21650800	Weak transcription	NHEK	skin
12	chr10:21645400-21651000	Weak transcription	HMEC	breast
13	chr10:21645600-21651000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:21645800-21647400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr10:21646000-21647000	Weak transcription	Placenta	Placenta
16	chr10:21646200-21646800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:21646200-21650600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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