Variant report

Variant	rs13385193
Chromosome Location	chr2:100599407-100599408
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	chr2:100597919..100600769-chr2:100602279..100603828,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10164818	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10165066	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10183465	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10185707	0.82[EUR][1000 genomes]
rs10187195	0.87[EUR][1000 genomes]
rs10189707	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10198062	0.82[EUR][1000 genomes]
rs10198187	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10211423	1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs11887136	0.86[EUR][1000 genomes]
rs11897706	0.83[EUR][1000 genomes]
rs13382597	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13383014	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13405987	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13410695	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13410884	0.86[EUR][1000 genomes]
rs13413309	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13416574	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs17023362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17023378	1.00[EUR][1000 genomes]
rs17023391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17023393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17352514	0.90[EUR][1000 genomes]
rs17436983	0.88[EUR][1000 genomes]
rs17437101	0.88[EUR][1000 genomes]
rs2001722	0.81[EUR][1000 genomes]
rs2309775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4129805	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4485586	0.88[EUR][1000 genomes]
rs4641993	0.83[EUR][1000 genomes]
rs55649403	0.97[EUR][1000 genomes]
rs55681051	0.97[EUR][1000 genomes]
rs56332326	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs57360658	0.84[EUR][1000 genomes]
rs58270548	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62149271	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62149296	0.88[EUR][1000 genomes]
rs62149302	0.88[EUR][1000 genomes]
rs62149303	0.88[EUR][1000 genomes]
rs62149304	0.90[EUR][1000 genomes]
rs62149305	0.88[EUR][1000 genomes]
rs62149307	0.88[EUR][1000 genomes]
rs62149310	0.88[EUR][1000 genomes]
rs62149311	0.87[EUR][1000 genomes]
rs62149314	0.86[EUR][1000 genomes]
rs62149316	0.82[EUR][1000 genomes]
rs6719214	0.90[EUR][1000 genomes]
rs6736239	0.97[EUR][1000 genomes]
rs72819147	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs72819157	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72819165	0.97[EUR][1000 genomes]
rs7425132	0.84[EUR][1000 genomes]
rs7576469	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7577040	0.84[EUR][1000 genomes]
rs9308832	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1003114	chr2:100480432-100601586	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13385193	IL1R1	cis	parietal	SCAN
rs13385193	RPL31	cis	cerebellum	SCAN
rs13385193	AFF3	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100550800-100618200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:100563200-100625400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:100564800-100617000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:100573800-100599600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:100577400-100618200	Weak transcription	Aorta	Aorta
6	chr2:100577800-100603400	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:100577800-100607400	Weak transcription	Thymus	Thymus
8	chr2:100577800-100623000	Weak transcription	Adipose Nuclei	Adipose
9	chr2:100577800-100623000	Weak transcription	Brain Angular Gyrus	brain
10	chr2:100578000-100616200	Weak transcription	Fetal Thymus	thymus
11	chr2:100582400-100608000	Weak transcription	Fetal Stomach	stomach
12	chr2:100583200-100608000	Strong transcription	Primary B cells from peripheral blood	blood
13	chr2:100587400-100599600	Weak transcription	Ovary	ovary
14	chr2:100587400-100601200	Weak transcription	Left Ventricle	heart
15	chr2:100587400-100623000	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr2:100587400-100623000	Weak transcription	Spleen	Spleen
17	chr2:100590400-100618000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:100591000-100607200	Weak transcription	Brain Germinal Matrix	brain
19	chr2:100591400-100604200	Weak transcription	Fetal Heart	heart
20	chr2:100591400-100605000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:100592200-100601400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:100592600-100601400	Strong transcription	Primary B cells from cord blood	blood
23	chr2:100592600-100626400	Weak transcription	NH-A	brain
24	chr2:100594600-100623000	Weak transcription	Gastric	stomach
25	chr2:100595800-100601200	Weak transcription	Fetal Brain Female	brain
26	chr2:100596600-100600600	Weak transcription	Fetal Brain Male	brain
27	chr2:100596600-100604600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:100597000-100601200	Weak transcription	Osteobl	bone
29	chr2:100597200-100601200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:100598400-100599800	Strong transcription	Dnd41	blood
31	chr2:100598400-100600400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:100598600-100604600	Weak transcription	Right Atrium	heart
33	chr2:100598600-100623000	Weak transcription	Lung	lung
34	chr2:100598800-100600200	Strong transcription	Primary hematopoietic stem cells	blood
35	chr2:100598800-100603600	Weak transcription	Primary T cells from cord blood	blood
36	chr2:100599000-100614000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:100599200-100601200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:100599400-100602200	Enhancers	Fetal Lung	lung

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