Variant report

Variant	rs493899
Chromosome Location	chr11:65747952-65747953
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65742158..65748813-chr11:65749011..65756801,11	MCF-7	breast:
2	chr1:156717397..156719936-chr11:65746740..65749009,2	MCF-7	breast:
3	chr11:65739309..65741332-chr11:65747619..65750098,2	MCF-7	breast:
4	chr11:65747825..65750124-chr11:65778940..65780987,2	MCF-7	breast:
5	chr11:65746618..65749014-chr11:65755089..65756613,2	K562	blood:
6	chr11:65746340..65748696-chr11:65818122..65820186,2	K562	blood:

Variant related genes	Relation type
ENSG00000254867	Chromatin interaction
ENSG00000175315	Chromatin interaction
ENSG00000087365	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11227368	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1151505	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1151512	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1192168	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1204649	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12792888	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12794370	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12797319	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1308733	0.85[EUR][1000 genomes]
rs14157	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1786175	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3016868	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35049625	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs470192	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs491973	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs501353	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs503524	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs528736	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs531612	0.81[EUR][1000 genomes]
rs538954	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs542332	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550435	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551659	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs552130	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs556643	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs559078	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55928757	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55994535	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56154109	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56239996	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs566590	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs593525	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs606978	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs613924	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs624273	0.83[EUR][1000 genomes]
rs632578	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs642293	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649000	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655744	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs659982	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs660118	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs679581	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs688862	0.83[EUR][1000 genomes]
rs7105628	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][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	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
2	nsv897762	chr11:65613218-65758854	Active TSS Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
3	nsv897765	chr11:65623708-65758854	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv832191	chr11:65632329-65806120	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv897769	chr11:65727799-65828625	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs493899	BANF1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65730600-65767800	Weak transcription	Right Atrium	heart
2	chr11:65731200-65748600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:65731200-65749600	Strong transcription	Fetal Intestine Small	intestine
4	chr11:65731400-65748000	Strong transcription	Thymus	Thymus
5	chr11:65731800-65749000	Strong transcription	Fetal Stomach	stomach
6	chr11:65732400-65748800	Strong transcription	Stomach Smooth Muscle	stomach
7	chr11:65732800-65748200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr11:65735200-65750600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr11:65735800-65756600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr11:65736400-65767400	Weak transcription	Psoas Muscle	Psoas
11	chr11:65737000-65748000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr11:65737600-65748000	Strong transcription	Fetal Muscle Leg	muscle
13	chr11:65737800-65756600	Weak transcription	Stomach Mucosa	stomach
14	chr11:65739200-65749600	Strong transcription	Fetal Brain Female	brain
15	chr11:65739600-65748000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr11:65739600-65748800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:65739600-65756400	Weak transcription	Fetal Kidney	kidney
18	chr11:65739800-65756400	Weak transcription	Hela-S3	cervix
19	chr11:65740600-65748000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:65740800-65748000	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr11:65741200-65765000	Weak transcription	NHDF-Ad	bronchial
22	chr11:65741400-65762000	Weak transcription	HSMMtube	muscle
23	chr11:65741600-65762000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:65742200-65759800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:65742800-65748000	Strong transcription	Primary T cells from cord blood	blood
26	chr11:65743000-65748000	Strong transcription	Fetal Intestine Large	intestine
27	chr11:65743000-65748200	Strong transcription	Brain Germinal Matrix	brain
28	chr11:65743000-65749200	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr11:65743000-65749400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr11:65743200-65748000	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr11:65743200-65748000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:65743200-65748000	Strong transcription	Esophagus	oesophagus
33	chr11:65743600-65748000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr11:65743800-65764800	Weak transcription	HSMM	muscle
35	chr11:65744600-65748000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:65745000-65764200	Weak transcription	HUVEC	blood vessel
37	chr11:65745200-65764800	Weak transcription	K562	blood
38	chr11:65745400-65750800	Weak transcription	HepG2	liver
39	chr11:65745400-65764800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr11:65745400-65765000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr11:65745600-65764200	Weak transcription	NH-A	brain
42	chr11:65745800-65756600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr11:65745800-65764800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr11:65746000-65764600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:65746800-65748000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr11:65746800-65756400	Weak transcription	Brain Substantia Nigra	brain
47	chr11:65746800-65765000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr11:65747000-65749000	Weak transcription	Brain Anterior Caudate	brain
49	chr11:65747000-65756400	Weak transcription	Primary B cells from cord blood	blood
50	chr11:65747000-65756400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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