Variant report

Variant	rs873491
Chromosome Location	chr11:65876570-65876571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65874283..65877270-chr11:65878896..65881081,3	MCF-7	breast:
2	chr11:65875746..65878415-chr11:65902728..65904507,2	MCF-7	breast:
3	chr11:65874972..65876623-chr11:65881726..65883847,2	K562	blood:
4	chr11:65836931..65839576-chr11:65872860..65876981,3	MCF-7	breast:
5	chr11:65869303..65872952-chr11:65875129..65877577,3	K562	blood:
6	chr11:65819625..65822322-chr11:65874052..65876918,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255038	Chromatin interaction
ENSG00000087365	Chromatin interaction
ENSG00000175115	Chromatin interaction
ENSG00000238752	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1049872	0.80[AMR][1000 genomes]
rs11823726	0.90[ASN][1000 genomes]
rs12419425	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12420458	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12803276	1.00[GIH][hapmap];0.92[MEX][hapmap]
rs17147325	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17147371	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]
rs1893316	1.00[GIH][hapmap];0.87[MEX][hapmap]
rs2452680	1.00[GIH][hapmap];0.87[MEX][hapmap]
rs33988687	0.82[AMR][1000 genomes]
rs3741370	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs3782081	0.92[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs3862387	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4930337	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4930340	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs503156	0.84[MEX][hapmap]
rs535752	0.84[MEX][hapmap]
rs55835736	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55944083	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56269595	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56314482	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs574153	0.84[MEX][hapmap]
rs61890288	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61890290	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61891827	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[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
rs873491	SNORD27	cis	cerebellum	SCAN
rs873491	SF3B2	cis	parietal	SCAN
rs873491	SF3B2	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65849200-65879600	Weak transcription	Aorta	Aorta
2	chr11:65851600-65882800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr11:65851800-65878800	Weak transcription	HSMM	muscle
4	chr11:65863800-65880200	Weak transcription	Fetal Stomach	stomach
5	chr11:65868400-65878400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:65868400-65879200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr11:65868400-65879200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr11:65868400-65879400	Weak transcription	Esophagus	oesophagus
9	chr11:65868400-65879400	Weak transcription	Ovary	ovary
10	chr11:65868400-65879600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr11:65868400-65879600	Weak transcription	Fetal Brain Female	brain
12	chr11:65868400-65879600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr11:65868600-65879200	Weak transcription	Pancreas	Pancrea
14	chr11:65868600-65879400	Weak transcription	Small Intestine	intestine
15	chr11:65868600-65879600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:65868600-65879600	Weak transcription	Colon Smooth Muscle	Colon
17	chr11:65868600-65893800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr11:65868800-65886200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr11:65869000-65878000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr11:65869000-65882800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr11:65869200-65876800	Weak transcription	Stomach Mucosa	stomach
22	chr11:65869200-65877000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr11:65869200-65877400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr11:65869200-65879600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr11:65869400-65877000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr11:65869800-65879400	Weak transcription	Brain Angular Gyrus	brain
27	chr11:65870000-65879200	Weak transcription	Thymus	Thymus
28	chr11:65870600-65879000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr11:65870800-65879400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr11:65872200-65878800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr11:65872200-65879600	Weak transcription	Brain Germinal Matrix	brain
32	chr11:65872400-65879000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr11:65872400-65879400	Weak transcription	Adipose Nuclei	Adipose
34	chr11:65873200-65878800	Genic enhancers	Primary T cells from cord blood	blood
35	chr11:65873400-65876800	Genic enhancers	Primary B cells from peripheral blood	blood
36	chr11:65873400-65877000	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr11:65873600-65876800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr11:65874600-65876600	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr11:65874600-65877600	Enhancers	Hela-S3	cervix
40	chr11:65874600-65879400	Weak transcription	Fetal Intestine Small	intestine
41	chr11:65874800-65877600	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr11:65874800-65879200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr11:65874800-65879200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr11:65874800-65879400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr11:65874800-65879400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr11:65874800-65879400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr11:65874800-65879400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr11:65874800-65879400	Weak transcription	Gastric	stomach
49	chr11:65874800-65879400	Weak transcription	Lung	lung
50	chr11:65874800-65879600	Weak transcription	Psoas Muscle	Psoas

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