Variant report

Variant	rs60109456
Chromosome Location	chr11:65742283-65742284
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65742003-65742292	GM12891	blood:	n/a	n/a
2	POLR2A	chr11:65742214-65742368	K562	blood:	n/a	n/a
3	POLR2A	chr11:65741908-65742370	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:65741814-65742311	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:65742012-65742406	SK-N-MC	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65742158..65748813-chr11:65749011..65756801,11	MCF-7	breast:
2	chr11:65741441..65743568-chr11:65744184..65746750,2	MCF-7	breast:
3	chr11:65714788..65716960-chr11:65740842..65742416,2	K562	blood:
4	chr11:65737150..65739313-chr11:65741413..65743660,2	MCF-7	breast:
5	chr11:65381324..65383343-chr11:65740916..65743548,2	MCF-7	breast:

No data

Variant related genes	Relation type
SART1	TF binding region
ENSG00000197136	Chromatin interaction
ENSG00000173327	Chromatin interaction
ENSG00000175467	Chromatin interaction
ENSG00000254867	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1047464	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10791835	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10791837	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10896073	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10896074	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11227370	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12363614	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2276132	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3759035	0.85[AMR][1000 genomes]
rs55947178	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7128076	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs735942	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs747526	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7934543	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7939253	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7939390	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7952056	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9735063	0.87[AMR][1000 genomes];0.81[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	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
rs60109456	BANF1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65729800-65746200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:65730600-65767800	Weak transcription	Right Atrium	heart
3	chr11:65731000-65744600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr11:65731200-65747400	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr11:65731200-65747800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr11:65731200-65748600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:65731200-65749600	Strong transcription	Fetal Intestine Small	intestine
8	chr11:65731400-65747600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:65731400-65747600	Strong transcription	Fetal Thymus	thymus
10	chr11:65731400-65748000	Strong transcription	Thymus	Thymus
11	chr11:65731600-65742400	Strong transcription	Primary T cells from cord blood	blood
12	chr11:65731600-65747400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:65731600-65747800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:65731800-65749000	Strong transcription	Fetal Stomach	stomach
15	chr11:65732000-65747200	Strong transcription	Lung	lung
16	chr11:65732400-65748800	Strong transcription	Stomach Smooth Muscle	stomach
17	chr11:65732800-65748200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr11:65735200-65750600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr11:65735800-65756600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr11:65736200-65744000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:65736400-65743200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:65736400-65767400	Weak transcription	Psoas Muscle	Psoas
23	chr11:65736800-65743400	Weak transcription	K562	blood
24	chr11:65736800-65744400	Weak transcription	HepG2	liver
25	chr11:65736800-65745000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr11:65736800-65747800	Strong transcription	Fetal Muscle Trunk	muscle
27	chr11:65737000-65748000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr11:65737200-65743200	Weak transcription	Aorta	Aorta
29	chr11:65737200-65744000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr11:65737200-65747800	Strong transcription	Placenta	Placenta
31	chr11:65737200-65747800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr11:65737600-65744800	Weak transcription	Small Intestine	intestine
33	chr11:65737600-65748000	Strong transcription	Fetal Muscle Leg	muscle
34	chr11:65737800-65742800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr11:65737800-65743400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr11:65737800-65744200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr11:65737800-65744600	Weak transcription	HUVEC	blood vessel
38	chr11:65737800-65756600	Weak transcription	Stomach Mucosa	stomach
39	chr11:65738000-65743200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr11:65738000-65743800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr11:65738200-65743200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr11:65738200-65743200	Weak transcription	Esophagus	oesophagus
43	chr11:65738200-65743200	Weak transcription	Pancreas	Pancrea
44	chr11:65738200-65743400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr11:65738200-65743600	Weak transcription	Colonic Mucosa	Colon
46	chr11:65738200-65743600	Weak transcription	Gastric	stomach
47	chr11:65738200-65744600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:65738200-65744800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr11:65739000-65747800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:65739200-65742400	Strong transcription	A549	lung

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