Variant report

Variant	rs477280
Chromosome Location	chr11:65835251-65835252
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:65834913-65836259	A549	lung:	n/a	chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
2	CTCF	chr11:65834974-65838748	SK-N-SH	brain:	n/a	chr11:65838478-65838491 chr11:65838476-65838494 chr11:65835874-65835887 chr11:65835872-65835890 chr11:65835867-65835888 chr11:65835873-65835889 chr11:65835877-65835885
3	POLR2A	chr11:65835192-65835624	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65654924..65660442-chr11:65834310..65838665,6	K562	blood:
2	chr11:65816864..65823380-chr11:65832037..65840391,16	MCF-7	breast:
3	chr11:65812201..65814006-chr11:65833921..65836110,2	K562	blood:
4	chr11:65665582..65668888-chr11:65835107..65838015,3	K562	blood:
5	chr11:65788482..65791914-chr11:65833749..65837289,3	MCF-7	breast:
6	chr11:65638895..65641565-chr11:65834356..65837225,2	K562	blood:
7	chr11:65833653..65835792-chr11:65836386..65838541,2	MCF-7	breast:
8	chr11:65756158..65757092-chr11:65835112..65836021,4	MCF-7	breast:
9	chr11:65654924..65661575-chr11:65833688..65838665,10	K562	blood:
10	chr11:65826244..65833224-chr11:65834439..65839387,11	MCF-7	breast:
11	chr11:65823620..65825685-chr11:65833626..65835266,2	MCF-7	breast:
12	chr11:65773321..65775670-chr11:65834388..65836189,2	K562	blood:

Variant related genes	Relation type
PACS1	TF binding region
ENSG00000175294	Chromatin interaction
ENSG00000238752	Chromatin interaction
ENSG00000255038	Chromatin interaction
ENSG00000175602	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000172638	Chromatin interaction
ENSG00000175229	Chromatin interaction
ENSG00000175115	Chromatin interaction
ENSG00000175592	Chromatin interaction
ENSG00000087365	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1049872	0.83[EUR][1000 genomes]
rs1203998	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12803276	0.83[EUR][1000 genomes]
rs2000672	0.82[EUR][1000 genomes]
rs2452680	0.82[EUR][1000 genomes]
rs33988687	0.83[EUR][1000 genomes]
rs34073119	0.82[EUR][1000 genomes]
rs34123790	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35611816	0.97[EUR][1000 genomes]
rs491618	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs503156	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs535752	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs547404	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs557799	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs570887	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs574153	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7480811	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs947847	0.85[AMR][1000 genomes];0.90[EUR][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	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	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs477280	SF3B2	cis	Whole Blood	GTEx
rs477280	SF3B2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65821000-65835600	Weak transcription	Right Atrium	heart
2	chr11:65821000-65836600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:65821000-65836600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:65821200-65835400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr11:65821200-65835600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:65821200-65836000	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr11:65821200-65836000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr11:65821200-65836000	Strong transcription	Fetal Intestine Large	intestine
9	chr11:65821200-65836000	Strong transcription	NHLF	lung
10	chr11:65821200-65836200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr11:65821200-65836600	Strong transcription	Fetal Stomach	stomach
12	chr11:65821400-65835400	Strong transcription	Stomach Smooth Muscle	stomach
13	chr11:65821400-65835600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:65821400-65835600	Strong transcription	Brain Germinal Matrix	brain
15	chr11:65821400-65835800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr11:65821400-65836600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:65821600-65835400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:65821600-65835400	Strong transcription	Fetal Thymus	thymus
19	chr11:65821600-65836000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr11:65821800-65835400	Strong transcription	Spleen	Spleen
21	chr11:65821800-65835800	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr11:65821800-65835800	Strong transcription	K562	blood
23	chr11:65821800-65836000	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr11:65821800-65836000	Strong transcription	Primary T cells from cord blood	blood
25	chr11:65821800-65836600	Strong transcription	Thymus	Thymus
26	chr11:65822000-65835400	Strong transcription	Primary B cells from cord blood	blood
27	chr11:65822000-65835400	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr11:65822000-65835400	Strong transcription	Brain Substantia Nigra	brain
29	chr11:65822000-65835400	Strong transcription	Fetal Brain Female	brain
30	chr11:65822000-65835600	Strong transcription	Brain Anterior Caudate	brain
31	chr11:65822000-65835600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:65822000-65835600	Strong transcription	Colonic Mucosa	Colon
33	chr11:65822000-65835600	Strong transcription	Gastric	stomach
34	chr11:65822000-65835600	Strong transcription	Rectal Smooth Muscle	rectum
35	chr11:65822000-65835600	Strong transcription	NHDF-Ad	bronchial
36	chr11:65822000-65835800	Strong transcription	Fetal Lung	lung
37	chr11:65822000-65835800	Strong transcription	Ovary	ovary
38	chr11:65822000-65835800	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr11:65822000-65836000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr11:65822000-65836000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr11:65822000-65836000	Strong transcription	HUVEC	blood vessel
42	chr11:65822000-65836000	Strong transcription	NH-A	brain
43	chr11:65822000-65836200	Strong transcription	Hela-S3	cervix
44	chr11:65822000-65836400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr11:65822000-65836400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:65822000-65836400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr11:65822200-65835400	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr11:65822200-65835600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr11:65822200-65835600	Strong transcription	HSMM	muscle
50	chr11:65822200-65835800	Strong transcription	Placenta Amnion	Placenta Amnion

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