Variant report

Variant	rs10840415
Chromosome Location	chr11:10464912-10464913
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:10464794..10466976-chr11:10476133..10477728,2	MCF-7	breast:
2	chr11:10464906..10468864-chr11:10475520..10479355,5	K562	blood:
3	chr11:10459654..10465823-chr11:10469269..10473470,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133805	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10840408	0.81[MEX][hapmap]
rs10840416	0.83[ASN][1000 genomes]
rs10840417	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11042805	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11821297	0.82[AMR][1000 genomes]
rs4909928	0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4909929	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7103258	1.00[JPT][hapmap];0.86[MEX][hapmap]
rs7107698	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72856176	0.82[AMR][1000 genomes]
rs72856182	0.94[EUR][1000 genomes]
rs7934278	0.92[CEU][hapmap]
rs7937289	0.81[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv896990	chr11:10458596-10514707	Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv3431765	chr11:10463326-10465324	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3475409	chr11:10464338-10470458	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3475420	chr11:10464352-10470454	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10840415	ST5	cis	parietal	SCAN
rs10840415	AMPD3	cis	cerebellum	SCAN
rs10840415	OR2AG1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10457600-10471800	Weak transcription	NHDF-Ad	bronchial
2	chr11:10459400-10465600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr11:10462600-10467400	Enhancers	Primary B cells from peripheral blood	blood
4	chr11:10462600-10467600	Enhancers	Fetal Thymus	thymus
5	chr11:10462800-10467600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr11:10463000-10467000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr11:10463000-10467000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:10463200-10465400	Enhancers	Primary B cells from cord blood	blood
9	chr11:10463400-10465000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:10463400-10466400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:10463600-10465400	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr11:10463800-10465600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr11:10464000-10465600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr11:10464000-10465600	Weak transcription	Primary T cells from cord blood	blood
15	chr11:10464000-10466200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr11:10464000-10466200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr11:10464000-10466200	Weak transcription	Dnd41	blood
18	chr11:10464000-10466400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr11:10464000-10466600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr11:10464000-10466600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:10464000-10467000	Weak transcription	Adipose Nuclei	Adipose
22	chr11:10464000-10471000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:10464000-10471000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr11:10464200-10466400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr11:10464600-10465800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr11:10464600-10471600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr11:10464800-10465000	Enhancers	GM12878-XiMat	blood
28	chr11:10464800-10465200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr11:10464800-10466200	Weak transcription	Thymus	Thymus
30	chr11:10464800-10466400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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