Variant report

Variant	rs13286025
Chromosome Location	chr9:15298768-15298769
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	chr9:15298408..15301257-chr9:15344895..15347811,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs13292233	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13293198	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13300981	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16932961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16932962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16932963	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16932968	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16932971	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16932980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16932982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2199599	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34905481	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs36086967	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3866794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3866795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3905248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4259499	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs562177	0.82[CHB][hapmap]
rs581080	0.82[CHB][hapmap]
rs59781734	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62570841	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62570851	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62570852	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs693223	0.82[CHB][hapmap]
rs7021480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022190	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035801	0.82[CHB][hapmap]
rs7038053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038333	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7042768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031340	chr9:15163004-15332769	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2761505	chr9:15274373-15319613	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv892624	chr9:15283761-15415461	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv613650	chr9:15296119-15378449	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv613651	chr9:15296355-15358157	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1015960	chr9:15296783-15380657	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13286025	GLUL	trans	lymphoblastoid	seeQTL
rs13286025	GPR183	trans	lymphoblastoid	seeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15287400-15303600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr9:15290800-15305600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:15290800-15306000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:15291200-15305600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:15294400-15306200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:15296600-15299000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr9:15296600-15299400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr9:15296600-15301200	Enhancers	Primary B cells from peripheral blood	blood
9	chr9:15296800-15299000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr9:15296800-15299000	Enhancers	Fetal Thymus	thymus
11	chr9:15296800-15305600	Weak transcription	Left Ventricle	heart
12	chr9:15297000-15299000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr9:15297000-15299400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr9:15297000-15299600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr9:15297000-15305200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr9:15297200-15298800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:15297200-15298800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr9:15297200-15298800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr9:15297200-15298800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:15297200-15300800	Enhancers	Primary hematopoietic stem cells	blood
21	chr9:15297200-15305600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr9:15297200-15305600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr9:15297200-15305600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr9:15297400-15298800	Weak transcription	Small Intestine	intestine
25	chr9:15297400-15299000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr9:15297400-15299000	Enhancers	HepG2	liver
27	chr9:15297400-15299400	Weak transcription	Psoas Muscle	Psoas
28	chr9:15297400-15299600	Weak transcription	HUVEC	blood vessel
29	chr9:15297400-15300200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:15297400-15300200	Weak transcription	Spleen	Spleen
31	chr9:15297400-15304800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr9:15297400-15305200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr9:15297400-15305600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr9:15297400-15305600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:15297400-15305600	Weak transcription	NHEK	skin
36	chr9:15297400-15305600	Weak transcription	NHLF	lung
37	chr9:15297400-15306000	Weak transcription	HSMM	muscle
38	chr9:15297600-15298800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr9:15297600-15298800	Weak transcription	Thymus	Thymus
40	chr9:15297600-15299800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:15297600-15300000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:15297600-15300200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr9:15297600-15300200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:15297600-15300200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr9:15297600-15300200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:15297600-15300200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr9:15297600-15301000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr9:15297600-15301000	Strong transcription	Fetal Stomach	stomach
49	chr9:15297600-15304600	Weak transcription	Stomach Mucosa	stomach
50	chr9:15297600-15305200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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