Variant report

Variant	rs17147371
Chromosome Location	chr11:65912524-65912525
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65909178..65910737-chr11:65912295..65914577,2	MCF-7	breast:
2	chr11:65904866..65907963-chr11:65908725..65912657,6	MCF-7	breast:
3	chr11:65911758..65913479-chr11:65914461..65916927,2	MCF-7	breast:
4	chr11:65835157..65840095-chr11:65905234..65913819,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175115	Chromatin interaction
ENSG00000255038	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11823726	0.93[ASN][1000 genomes]
rs12419425	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12420458	0.90[ASN][1000 genomes]
rs12803276	1.00[GIH][hapmap];0.92[MEX][hapmap]
rs17147325	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1893316	1.00[GIH][hapmap];0.87[MEX][hapmap]
rs2452680	1.00[GIH][hapmap];0.87[MEX][hapmap]
rs3741370	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs3782081	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs3862387	0.88[ASN][1000 genomes]
rs4930337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4930340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs503156	0.84[MEX][hapmap]
rs535752	0.84[MEX][hapmap]
rs55835736	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55944083	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56269595	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56314482	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs574153	0.84[MEX][hapmap]
rs61890288	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61890290	0.90[ASN][1000 genomes]
rs61891827	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs873491	0.86[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17147371	SF3B2	cis	cerebellum	SCAN
rs17147371	SNORD27	cis	cerebellum	SCAN
rs17147371	SF3B2	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65895000-65913800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr11:65895000-65917600	Weak transcription	HSMM	muscle
3	chr11:65895200-65913000	Weak transcription	Psoas Muscle	Psoas
4	chr11:65896600-65912800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr11:65898400-65913000	Weak transcription	Spleen	Spleen
6	chr11:65901000-65919400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr11:65902000-65912800	Weak transcription	Right Atrium	heart
8	chr11:65905200-65913000	Weak transcription	Aorta	Aorta
9	chr11:65905200-65947000	Weak transcription	Fetal Lung	lung
10	chr11:65905400-65939600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr11:65905600-65912600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr11:65905800-65924200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:65905800-65952800	Weak transcription	Fetal Stomach	stomach
14	chr11:65906000-65912800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr11:65906000-65960200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr11:65909000-65913400	Enhancers	Stomach Mucosa	stomach
17	chr11:65909600-65913000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr11:65909800-65912800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr11:65909800-65913200	Enhancers	Duodenum Mucosa	Duodenum
20	chr11:65909800-65914200	Weak transcription	Esophagus	oesophagus
21	chr11:65909800-65914200	Enhancers	HepG2	liver
22	chr11:65910000-65912800	Weak transcription	Gastric	stomach
23	chr11:65910000-65913400	Enhancers	Fetal Intestine Small	intestine
24	chr11:65910000-65914000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:65910000-65914200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:65910000-65939600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr11:65910200-65913800	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr11:65910400-65913400	Genic enhancers	Primary B cells from peripheral blood	blood
29	chr11:65910400-65913800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr11:65910400-65916000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr11:65910400-65918600	Weak transcription	HSMMtube	muscle
32	chr11:65910400-65927000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:65910600-65917400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:65910600-65939600	Weak transcription	NHDF-Ad	bronchial
35	chr11:65910800-65913400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr11:65910800-65917400	Weak transcription	NHLF	lung
37	chr11:65910800-65917600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:65911000-65918800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:65911000-65924400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr11:65911000-65924400	Weak transcription	NHEK	skin
41	chr11:65911000-65924600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr11:65911000-65939400	Weak transcription	NH-A	brain
43	chr11:65911000-65943200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr11:65911200-65912800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr11:65911400-65912800	Weak transcription	Pancreas	Pancrea
46	chr11:65911800-65912600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr11:65911800-65914200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr11:65911800-65916600	Weak transcription	K562	blood
49	chr11:65912000-65912600	Weak transcription	A549	lung
50	chr11:65912000-65912800	Genic enhancers	Primary B cells from cord blood	blood

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