Variant report

Variant	rs1115508
Chromosome Location	chr11:65923149-65923150
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	chr11:65902080..65904431-chr11:65921918..65923444,2	MCF-7	breast:
2	chr11:65921627..65923245-chr11:65927449..65930072,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10791865	0.94[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs10896104	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151537	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1151539	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151540	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.80[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203798	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1717669	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1892939	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2508657	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3016319	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs472518	0.85[LWK][hapmap]
rs474005	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs521109	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs527897	0.91[LWK][hapmap]
rs528842	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs555360	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs555853	0.83[ASN][1000 genomes]
rs556595	1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs708471	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs708472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs801731	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs801734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs801735	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs801736	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs801737	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs801739	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs801741	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9326370	1.00[CEU][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	esv1809358	chr11:65916558-65935189	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv1811442	chr11:65922589-65939026	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv1804701	chr11:65922589-65957003	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv1813498	chr11:65922589-65957003	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1115508	RAB1B	cis	parietal	SCAN
rs1115508	RP11-867G23.1	cis	Muscle Skeletal	GTEx
rs1115508	C11orf2	cis	parietal	SCAN
rs1115508	MRGPRF	cis	parietal	SCAN
rs1115508	RAB1B	cis	cerebellum	SCAN
rs1115508	SNX32	cis	parietal	SCAN
rs1115508	INTS5	cis	cerebellum	SCAN
rs1115508	KLC2	cis	Muscle Skeletal	GTEx
rs1115508	PACS1	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65905200-65947000	Weak transcription	Fetal Lung	lung
2	chr11:65905400-65939600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr11:65905800-65924200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr11:65905800-65952800	Weak transcription	Fetal Stomach	stomach
5	chr11:65906000-65960200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr11:65910000-65939600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:65910400-65927000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:65910600-65939600	Weak transcription	NHDF-Ad	bronchial
9	chr11:65911000-65924400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr11:65911000-65924400	Weak transcription	NHEK	skin
11	chr11:65911000-65924600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:65911000-65939400	Weak transcription	NH-A	brain
13	chr11:65911000-65943200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:65912800-65924400	Weak transcription	A549	lung
15	chr11:65913200-65927000	Weak transcription	Right Ventricle	heart
16	chr11:65913200-65927200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr11:65913400-65924400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr11:65913400-65924400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr11:65913400-65929800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr11:65913400-65951000	Weak transcription	Spleen	Spleen
21	chr11:65914000-65924400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr11:65914200-65939600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr11:65914600-65929600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr11:65914800-65927000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr11:65917800-65924400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr11:65918000-65949200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:65918400-65924400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr11:65918600-65924600	Weak transcription	Osteobl	bone
29	chr11:65918800-65926800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr11:65919000-65924400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr11:65919000-65924400	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:65919000-65927000	Weak transcription	Right Atrium	heart
33	chr11:65919000-65927000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr11:65919000-65928600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr11:65919000-65928600	Weak transcription	Left Ventricle	heart
36	chr11:65919000-65939800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr11:65920200-65928000	Weak transcription	Primary T cells from cord blood	blood
38	chr11:65920400-65924200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:65920400-65924400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr11:65920400-65954800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr11:65920800-65924400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:65921000-65924400	Weak transcription	Hela-S3	cervix
43	chr11:65921000-65932400	Weak transcription	Primary B cells from cord blood	blood
44	chr11:65922000-65923400	Enhancers	HepG2	liver
45	chr11:65922800-65923400	Enhancers	GM12878-XiMat	blood
46	chr11:65922800-65926800	Weak transcription	Fetal Brain Male	brain
47	chr11:65922800-65927000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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