Variant report

Variant	rs13091509
Chromosome Location	chr3:23970695-23970696
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	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174738	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11717862	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13095392	0.85[EUR][1000 genomes]
rs4131403	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4241514	0.88[EUR][1000 genomes]
rs4241515	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4241517	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4241520	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4321479	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4589882	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4619734	0.88[EUR][1000 genomes]
rs4858094	0.86[EUR][1000 genomes]
rs4858095	0.88[EUR][1000 genomes]
rs4858098	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858551	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4858553	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4858565	0.83[EUR][1000 genomes]
rs4858567	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858569	0.84[ASN][1000 genomes]
rs62253379	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6419846	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6550814	0.93[ASN][1000 genomes]
rs6550815	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6550819	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6550823	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6550824	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6764154	0.86[EUR][1000 genomes]
rs6779476	0.88[EUR][1000 genomes]
rs6790557	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6794922	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7371944	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7431301	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7636810	0.98[ASN][1000 genomes]
rs9845287	0.86[EUR][1000 genomes]
rs9853532	0.97[ASN][1000 genomes]
rs9863320	0.83[EUR][1000 genomes]
rs9882735	0.85[EUR][1000 genomes];0.86[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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23961800-23972800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:23961800-23980200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:23962000-23972800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:23962000-23974800	Weak transcription	Brain Substantia Nigra	brain
5	chr3:23962000-23977800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:23962000-23985600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:23963000-23975200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:23963200-23973200	Weak transcription	GM12878-XiMat	blood
9	chr3:23963200-23976000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:23963600-23973200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr3:23963800-23971000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr3:23963800-23973000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:23963800-23978400	Weak transcription	Aorta	Aorta
14	chr3:23964000-23974600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:23964200-23985000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:23964400-23973200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:23964400-23974400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:23965800-23973800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:23970400-23972800	Weak transcription	K562	blood
20	chr3:23970400-23973000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:23970400-23973200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:23970400-23978600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:23970600-23972800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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