Variant report

Variant	rs13402299
Chromosome Location	chr2:100659409-100659410
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	chr2:100658557..100661534-chr2:100689369..100692116,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10192951	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10209201	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12996621	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13001130	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13001783	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13020141	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13033732	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13402289	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430705	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17023468	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1821830	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2118281	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34040706	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34714421	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35300735	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35730185	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35774174	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35840153	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35869550	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4851243	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4851244	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4851250	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56037757	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56935201	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58683655	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59447631	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60311127	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60697219	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6750720	0.85[ASN][1000 genomes]
rs71413861	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7572939	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7596359	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9308833	0.80[ASN][1000 genomes]
rs9784000	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13402299	AFF3	cis	parietal	SCAN
rs13402299	MGAT4A	cis	parietal	SCAN
rs13402299	C2orf15	cis	parietal	SCAN
rs13402299	C2orf64	cis	cerebellum	SCAN
rs13402299	SNRNP200	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100633600-100660600	Weak transcription	Lung	lung
2	chr2:100639000-100660600	Weak transcription	Primary T cells from cord blood	blood
3	chr2:100644600-100668400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:100646400-100662600	Weak transcription	Gastric	stomach
5	chr2:100648200-100666800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:100651800-100659600	Weak transcription	Left Ventricle	heart
7	chr2:100652800-100661400	Weak transcription	Ovary	ovary
8	chr2:100653200-100667200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:100654800-100668200	Weak transcription	Thymus	Thymus
10	chr2:100655800-100661800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:100656400-100680000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:100656600-100686600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:100656800-100662800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:100657000-100661000	Weak transcription	Fetal Heart	heart
15	chr2:100657200-100661800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:100657400-100659800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:100657600-100660200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:100657800-100664400	Enhancers	Fetal Brain Male	brain
19	chr2:100658000-100660000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr2:100658200-100662600	Weak transcription	Fetal Lung	lung
21	chr2:100658400-100660000	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr2:100658400-100660600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr2:100658400-100661000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:100658600-100659800	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr2:100658600-100659800	Weak transcription	Fetal Brain Female	brain
26	chr2:100658800-100659800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr2:100658800-100660400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:100658800-100660600	Genic enhancers	Primary B cells from peripheral blood	blood
29	chr2:100658800-100668400	Weak transcription	Brain Germinal Matrix	brain
30	chr2:100659000-100659600	Genic enhancers	Primary B cells from cord blood	blood
31	chr2:100659000-100659800	Enhancers	Adipose Nuclei	Adipose
32	chr2:100659000-100660400	Weak transcription	Brain Substantia Nigra	brain
33	chr2:100659000-100661800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:100659400-100660600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:100659400-100680000	Weak transcription	Stomach Smooth Muscle	stomach

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