Variant report

Variant	rs17352808
Chromosome Location	chr2:100667168-100667169
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	chr2:100664977..100666534-chr2:100666677..100669564,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10177007	0.83[EUR][1000 genomes]
rs10185707	0.91[EUR][1000 genomes]
rs10198062	0.91[EUR][1000 genomes]
rs10199628	0.83[EUR][1000 genomes]
rs10211423	1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs13392222	0.97[EUR][1000 genomes]
rs17023453	0.98[EUR][1000 genomes]
rs17023459	0.98[EUR][1000 genomes]
rs17023512	0.82[EUR][1000 genomes]
rs17023516	0.82[EUR][1000 genomes]
rs17352514	0.85[EUR][1000 genomes]
rs17352745	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17352801	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17436983	0.84[EUR][1000 genomes]
rs17437101	0.87[EUR][1000 genomes]
rs17437248	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17437282	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17437338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2309776	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4485586	0.87[EUR][1000 genomes]
rs62149303	0.83[EUR][1000 genomes]
rs62149304	0.85[EUR][1000 genomes]
rs62149305	0.87[EUR][1000 genomes]
rs62149307	0.87[EUR][1000 genomes]
rs62149310	0.87[EUR][1000 genomes]
rs62149311	0.86[EUR][1000 genomes]
rs62149314	0.86[EUR][1000 genomes]
rs62149316	0.93[EUR][1000 genomes]
rs62149319	0.98[EUR][1000 genomes]
rs62149320	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62149321	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62149341	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62149343	0.96[EUR][1000 genomes]
rs62149348	0.86[EUR][1000 genomes]
rs62150260	0.82[EUR][1000 genomes]
rs6719214	0.85[EUR][1000 genomes]
rs6743817	0.83[EUR][1000 genomes]
rs6745099	0.82[EUR][1000 genomes]
rs6748652	0.82[EUR][1000 genomes]
rs6750214	0.99[EUR][1000 genomes]
rs72819167	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72819176	0.81[EUR][1000 genomes]
rs72819177	0.82[EUR][1000 genomes]
rs72819180	0.81[EUR][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	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17352808	AFF3	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100644600-100668400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr2:100653200-100667200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:100654800-100668200	Weak transcription	Thymus	Thymus
4	chr2:100656400-100680000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:100656600-100686600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:100658800-100668400	Weak transcription	Brain Germinal Matrix	brain
7	chr2:100659400-100680000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:100659800-100671600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:100660000-100669000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr2:100660600-100678200	Weak transcription	Fetal Muscle Leg	muscle
11	chr2:100660800-100668800	Weak transcription	Lung	lung
12	chr2:100661600-100668800	Weak transcription	Fetal Brain Female	brain
13	chr2:100661800-100667200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:100661800-100668400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:100661800-100670400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:100662200-100684800	Weak transcription	Ovary	ovary
17	chr2:100662800-100667400	Weak transcription	Dnd41	blood
18	chr2:100662800-100674200	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:100663000-100670400	Weak transcription	Gastric	stomach
20	chr2:100663000-100680800	Weak transcription	Fetal Kidney	kidney
21	chr2:100663000-100682200	Weak transcription	Fetal Heart	heart
22	chr2:100663400-100671600	Weak transcription	Primary T cells from cord blood	blood
23	chr2:100664400-100667200	Weak transcription	Fetal Brain Male	brain
24	chr2:100664400-100699600	Weak transcription	Aorta	Aorta
25	chr2:100664800-100668800	Weak transcription	Fetal Lung	lung
26	chr2:100665600-100667400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:100665800-100669200	Weak transcription	Left Ventricle	heart
28	chr2:100666400-100672800	Weak transcription	NH-A	brain
29	chr2:100666800-100671800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:100666800-100675000	Strong transcription	Primary B cells from cord blood	blood
31	chr2:100666800-100675800	Strong transcription	Primary B cells from peripheral blood	blood
32	chr2:100667000-100667200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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