Variant report

Variant	rs7289526
Chromosome Location	chr22:32797959-32797960
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	chr22:32791211..32793913-chr22:32796034..32798432,2	MCF-7	breast:

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs13110	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16990340	1.00[AMR][1000 genomes]
rs16990363	0.86[ASW][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs35003092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55726161	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56005103	0.87[AFR][1000 genomes]
rs56088001	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56164445	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56241612	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56257111	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56273567	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56300131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56304230	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56393759	1.00[AMR][1000 genomes]
rs56835150	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56870764	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56946080	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57040236	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57313377	0.97[AFR][1000 genomes]
rs57467712	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5749414	0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs57526188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57670657	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58329990	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58406751	0.87[AFR][1000 genomes]
rs58747874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58917959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59272508	0.85[AFR][1000 genomes]
rs59540071	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59540535	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59570290	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59814970	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5998441	1.00[AMR][1000 genomes]
rs60284718	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60614590	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61036457	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61060987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61702109	1.00[AMR][1000 genomes]
rs7284713	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7284743	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7285750	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7288743	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7289656	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7290295	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7293064	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881645	1.00[AMR][1000 genomes]
rs73881659	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881660	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881661	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881662	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881663	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881664	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881665	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881666	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881668	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881669	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881670	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881671	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881673	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881674	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881675	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881676	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881677	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881678	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881701	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73881702	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8139487	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8139992	0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8141096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8141141	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9680823	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1064737	chr22:32603912-32829725	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1066118	chr22:32779078-32815334	Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7289526	RFPL3S	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32780800-32806400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr22:32780800-32806400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:32781200-32798200	Strong transcription	Thymus	Thymus
4	chr22:32781200-32799200	Strong transcription	Duodenum Smooth Muscle	Duodenum
5	chr22:32781200-32801200	Strong transcription	Fetal Stomach	stomach
6	chr22:32781200-32802200	Strong transcription	Primary B cells from peripheral blood	blood
7	chr22:32781200-32803200	Strong transcription	Duodenum Mucosa	Duodenum
8	chr22:32781200-32804000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr22:32781200-32804200	Strong transcription	Stomach Smooth Muscle	stomach
10	chr22:32781200-32804600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr22:32781200-32804600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr22:32781200-32804800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr22:32781200-32805000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr22:32781200-32805400	Strong transcription	Fetal Muscle Leg	muscle
15	chr22:32781200-32806600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr22:32781400-32798200	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr22:32781400-32798200	Strong transcription	Brain Anterior Caudate	brain
18	chr22:32781400-32798200	Strong transcription	NH-A	brain
19	chr22:32781400-32799200	Strong transcription	Lung	lung
20	chr22:32781400-32801200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr22:32781400-32802600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr22:32781400-32802600	Strong transcription	GM12878-XiMat	blood
23	chr22:32781400-32802600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr22:32781400-32803200	Strong transcription	Adipose Nuclei	Adipose
25	chr22:32781400-32803200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr22:32781400-32803600	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr22:32781400-32803800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr22:32781400-32803800	Strong transcription	Liver	Liver
29	chr22:32781400-32804400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr22:32781400-32804600	Strong transcription	Fetal Thymus	thymus
31	chr22:32781400-32804600	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr22:32781400-32804600	Strong transcription	Dnd41	blood
33	chr22:32781400-32804800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr22:32781400-32804800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr22:32781400-32804800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr22:32781400-32804800	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr22:32781400-32805000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr22:32781400-32805000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr22:32781400-32805000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr22:32781400-32805000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr22:32781400-32805000	Strong transcription	Fetal Intestine Large	intestine
42	chr22:32781400-32805000	Strong transcription	Fetal Lung	lung
43	chr22:32781400-32805000	Strong transcription	Fetal Muscle Trunk	muscle
44	chr22:32781400-32805000	Strong transcription	Left Ventricle	heart
45	chr22:32781400-32805000	Strong transcription	Osteobl	bone
46	chr22:32781400-32805200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr22:32781400-32805200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr22:32781400-32805600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr22:32781400-32806400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr22:32781400-32806600	Strong transcription	Placenta	Placenta

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